Commit 66062843 authored by Yi Sun's avatar Yi Sun

adding help contents

parent 5f7ee093
<tool id="cp318" name="Cellprofiler" version="3.1.8">
<description>Run pipeline</description>
<tool id="cp319" name="Cellprofiler" version="19.05">
<description>Run a CellProfiler v3.1.9 pipeline</description>
<requirements>
<requirement type="package" version="3.1.8">cellprofiler</requirement>
<requirement type="package" version="3.1.9">cellprofiler</requirement>
</requirements>
<!-- ln -s '$filename' ./input/$i.tiff && -->
<!-- unzip $inputType.inputdir -d input && -->
<!-- ln -s '${filename.element_identifier}' ./input/$filename.element_identifier && -->
<command><![CDATA[
mkdir output &&
mkdir input &&
mkdir -p output &&
mkdir -p input &&
#if $inputType.iType =="z"
unzip $inputType.inputdir -d input &&
......@@ -39,9 +36,6 @@
<outputs>
<data format="txt" name="out">
<discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
<!-- <discover_datasets pattern="CUSTOM_(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="subdir1" visible="true" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv" ext="tabular" visible="true" /> -->
</data>
</outputs>
......@@ -52,7 +46,18 @@
</tests>
<help>
This tool runs a cellprofiler pipeline.
This tool runs a complete Cellprofiler v3.1.9 pipeline file. It takes a pipeline file and images from Galaxy history as input and generates its output files in Galaxy history. The input images can be a single zip file or multiple files.
*** Parameters ***
images: single zip file or multi-select image files
pipeline: CellProfiler v3.1.9 pipeline file(.cppipe) file.
*** Note ***
Only version v3.1.9 pipeline can be run, other versions may cause problems.
</help>
</tool>
<tool id="cp-common" name="Common modules" version="19.05">
<description>Build pipeline section for the first 4 compulsory modules</description>
<tool id="cp-common" name="Common " version="19.05">
<description>CellProfiler v3.1.9 modules Images,Metadata, NameAndTypes, Groups </description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -376,8 +376,20 @@ with open("output","w") as f:
<tests>
</tests>
<help>
This tool builds a Cellprofiler pipeline file with 4 compulsary modules, Images, Metadata, NamesAndTypes and Groups
<help>
This tool builds a Cellprofiler pipeline file with headers and 4 compulsary modules, 'Images', 'Metadata', 'NamesAndTypes' and 'Groups'.
No input parameters are needed for this tool. The rest CP modules will build based on the output of this file.
Images: use the Images module to compile a list of files that you want to analyze.
Metadata: optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements.
NamesAndTypes: allows you to assign a meaningful name to each image by which other modules will refer to it.
Groups: optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.
</help>
</tool>
<tool id="cp-convertobjectstoimage" name="ConvertObjectsToImage Module" version="19.05">
<description>Build pipeline section ConvertObjectsToImage</description>
<tool id="cp-convertobjectstoimage" name="ConvertObjectsToImage" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -33,9 +33,9 @@ def writecoti():
f.write(FOURSPACES+"Select the color format:"+color_format+NEWLINE)
if color_format=="Color":
f.write(FOURSPACES+"Select the colormap:"+ params['con_color_format']['color_map'])
f.write(FOURSPACES+"Select the colormap:"+ params['con_color_format']['color_map'] +NEWLINE)
else:
f.write(FOURSPACES+"Select the colormap:Default")
f.write(FOURSPACES+"Select the colormap:Default" + NEWLINE)
with open(input_pipeline) as fin:
lines = fin.readlines()
......@@ -64,7 +64,7 @@ f.close()
<conditional name="con_color_format">
<param name="color_format" type="select" label="Select the color format">
<option value="Color">Color</option>
<option value="Binary(black &amp; white)">Binary (black &amp; white)</option>
<option value="Binary (black &amp; white)">Binary (black &amp; white)</option>
<option value="Grayscale">Grayscale</option>
<option value="unit16">unit16</option>
<sanitizer sanitize="false"/>
......@@ -137,7 +137,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -148,7 +148,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with ConvertObjectsToImage module
This tool append the ConvertObjectsToImage module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-displaydataonimage" name="DisplayDataOnImage Module" version="19.05">
<description>Build pipeline section DisplayDataOnImage</description>
<tool id="cp-displaydataonimage" name="DisplayDataOnImage" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -261,7 +261,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -272,7 +272,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with DisplayDataOnImage module
This tool append the DisplayDataOnImage module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-enhanceorsuppressfeatures" name="EnhanceOrSuppressFeatures Module" version="19.05">
<description>Build pipeline section EnhanceOrSuppressFeatures</description>
<tool id="cp-enhanceorsuppressfeatures" name="EnhanceOrSuppressFeatures" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -223,7 +223,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -234,7 +234,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureTexture module
This tool append the EnhanceOrSuppressFeatures module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-exporttospreadsheet" name="ExportToSpreadsheet Module" version="19.05">
<description>Build pipeline section ExportToSpreadsheet</description>
<tool id="cp-exporttospreadsheet" name="ExportToSpreadsheet" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -53,7 +53,12 @@ def write_etss():
if export_all_measurements == "Yes":
f.write(FOURSPACES+"Export all measurement types?:"+export_all_measurements+NEWLINE)
f.write(FOURSPACES+"Press button to select measurements:"+NEWLINE)
if 'select_measurements' in params['con_measurement_export']:
f.write(FOURSPACES+"Press button to select measurements:"+ params['con_measurement_export']['select_measurements']+NEWLINE)
else:
f.write(FOURSPACES+"Press button to select measurements:"+NEWLINE)
f.write(FOURSPACES+"Representation of Nan/Inf:"+params["represent_nan"]+NEWLINE)
f.write(FOURSPACES+"Add a prefix to file names?:"+params["con_prefix"]["add_prefix"]+NEWLINE)
......@@ -199,7 +204,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with just the ExportToSpreadsheet module
This tool append the ExportToSpreadsheet module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-graytocolor" name="GrayToColor Module" version="19.05">
<description>Build pipeline section GrayToColor</description>
<tool id="cp-graytocolor" name="GrayToColor" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -222,7 +222,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -233,7 +233,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureTexture module
This tool append the GrayToColor module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-identifyprimaryobjects" name="IdentifyPrimaryObjects Module" version="19.05">
<description>Build pipeline section IdentifyPrimaryObject module</description>
<tool id="cp-identifyprimaryobjects" name="IdentifyPrimaryObjects" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -15,7 +15,7 @@
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
<param name="discard_touching_border" type="select" display="radio" label="Discard objects touching the image?">
<param name="discard_touching_border" type="select" display="radio" label="Discard objects touching the border of the image?">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
......@@ -32,7 +32,7 @@
</when>
</conditional>
<conditional name="con_min_distance">
<param name="min_distance" type="select" display="radio" label="automcatically calculate minimum allowed distance between local maxima?">
<param name="min_distance" type="select" display="radio" label="Automatically calculate minimum allowed distance between local maxima?">
<option value="Yes">Yes</option>
<option value="No">No</option>
</param>
......@@ -317,7 +317,21 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with IdentifyPrimaryObjects module
This tool append the IdentifyPrimaryObjects module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
Identify the nuclei from the DNA channel.
PARAMS:
- Typical diameter of objects (Min,Max)
- Method to distinguish clumped objects: Shape/None. With Shape, the distance between the 2 centers can be changed.
</help>
</tool>
<tool id="cp-maskimage" name="MaskImage Module" version="19.05">
<description>Build pipeline section MeasureObjectSizeShape</description>
<tool id="cp-maskimage" name="MaskImage" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -90,7 +90,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -101,7 +101,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MaskImage module
This tool append the MaskImage module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measuregranularity" name="MeasureGranularity Module" version="19.05">
<description>Build pipeline section MeasureGranularity</description>
<tool id="cp-measuregranularity" name="MeasureGranularity" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -87,7 +87,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -98,7 +98,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureGranularity module
This tool append the MeasureGranularity module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measureimageareaoccupied" name="MeasureImageAreaOccupied Module" version="19.05">
<description>Build pipeline section MeasureImageAreaOccupied</description>
<tool id="cp-measureimageareaoccupied" name="MeasureImageAreaOccupied" version="19.05">
<description>module of Cellprofiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -84,7 +84,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -95,7 +95,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureObjectSizeShape module
This tool append the MeasureImageAreaOccupied module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measureimageintensity" name="MeasureImageIntensity Module" version="19.05">
<description>Build pipeline section MeasureImageIntensity</description>
<tool id="cp-measureimageintensity" name="MeasureImageIntensity" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -88,7 +88,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -99,7 +99,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureImageIntensity module
This tool append the MeasureImageIntensity module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measureimagequality" name="MeasureImageQuality Module" version="19.05">
<description>Build pipeline section MeasureImageQuality</description>
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -219,7 +219,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -230,7 +230,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureImageQuality module
This tool append the MeasureImageQuality module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measureobjectintensity" name="MeasureObjectIntensity Module" version="19.05">
<description>Build pipeline section MeasureObjectIntensity</description>
<tool id="cp-measureobjectintensity" name="MeasureObjectIntensity" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -70,7 +70,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -81,7 +81,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureObjectIntensity module
This tool append the MeasureObjectIntensity module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measureobjectsizeshape" name="MeasureObjectSizeShape Module" version="19.05">
<description>Build pipeline section MeasureObjectSizeShape</description>
<tool id="cp-measureobjectsizeshape" name="MeasureObjectSizeShape" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -63,7 +63,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -74,7 +74,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureObjectSizeShape module
This tool append the MeasureObjectSizeShape module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-measuretexture" name="MeasureTexture Module" version="19.05">
<description>Build pipeline section MeasureTexture</description>
<tool id="cp-measuretexture" name="MeasureTexture" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -106,7 +106,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -117,7 +117,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with MeasureTexture module
This tool append the MeasureTexture module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-relateobjects" name="RelateObjects Module" version="19.05">
<description>Build pipeline section RelateObjects</description>
<tool id="cp-relateobjects" name="RelateObjects" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -129,7 +129,7 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
......@@ -140,7 +140,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with RelateObjects module
This tool append the RelateObjects module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
<tool id="cp-saveimages" name="SaveImages Module" version="19.05">
<description>Build pipeline section SaveImages</description>
<tool id="cp-saveimages" name="SaveImages" version="19.05">
<description>module of CellProfiler v3.1.9</description>
<requirements>
<requirement type="package" version="2.7.16">python</requirement>
</requirements>
......@@ -80,7 +80,7 @@ def writesi():
append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
f.write(FOURSPACES + "Number of digits:" + no_of_digits + NEWLINE)
f.write(FOURSPACES + "Append a suffix to the image file name?:" + no_of_digits + NEWLINE)
f.write(FOURSPACES + "Append a suffix to the image file name?:" + append_suffix + NEWLINE)
f.write(FOURSPACES + "Text to append to the image name:" + text_append + NEWLINE)
save_format = params['con_type_of_image']['con_save_file_format']['file_format']
......@@ -92,7 +92,8 @@ def writesi():
else:
bit_depth ="8-bit integer"
f.write(FOURSPACES + "Output file location:" + params['output_location'] + NEWLINE)
f.write(FOURSPACES + "Output file location:Default Output Folder\\x7Coutput" + NEWLINE)
f.write(FOURSPACES + "Image bit depth:" + bit_depth + NEWLINE)
......@@ -123,7 +124,7 @@ f.close()
</configfile>
</configfiles>
<command><![CDATA[
python $script_file $inputs $input_pipeline
python $script_file $inputs $input_pipeline
]]></command>
<inputs>
......@@ -182,17 +183,17 @@ f.close()
<param name="single_file_name" label="Enter single_file_name" type="text"/>
</when>
</conditional>
<param name="output_location" label="Output file location" type="select" >
<!-- <param name="output_location" label="Output file location" type="select" >
<option value="Same folder as image">Same folder as image</option>
</param>
</param> -->
<param name="overwrite_without_warning" label="Overwrite existing files without warning?" type="select" >
<option value="No">No</option>
<option value="Yes">Yes</option>
</param>
<param name="when_to_save" label="When to save" type="select" >
<option value="Every cyle">Every cyle</option>
<option value="First cyle">First cyle</option>
<option value="Last cyle">Last cyle</option>
<option value="Every cycle">Every cycle</option>
<option value="First cycle">First cycle</option>
<option value="Last cycle">Last cycle</option>
</param>
<param name="record_info" label="Record the file and path information to the saved image?" type="select" display="radio">
<option value="No">No</option>
......@@ -204,8 +205,9 @@ f.close()
</inputs>
<outputs>
<data name="out_file" from_work_dir="output" format="txt" hidden="false">
<data name="out_file" from_work_dir="output" format="txt" hidden="true">
</data>
</outputs>
<stdio>
......@@ -215,7 +217,13 @@ f.close()
</tests>
<help>
This tool builds a Cellprofiler pipeline with SaveImages module
This tool append the SaveImages module section to an existing pipeline file (.cppipe).
Input: existing pipeline file
Output: new pipelie file
Combine this tool with "Common" and "CellProfiler" together to run the module alone.
</help>
</tool>
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