Commit f10d7e08 authored by Charles Girardot's avatar Charles Girardot

Merge branch 'master' of git.embl.de:grp-gbcs/Je

parents 1c14c1ec 54ad8be9
Je
--
Additional documentation and support can be found at http://gbcs.embl.de/je
The Je tool suite
=================
......
# HowTo update the toolshed repository
After linting/testing your update using ``planemo test`` and ``planemo serve`` you can upload the changes to the toolshed repos.
For this you need to have the credentials or api_key of our ``gbcs-embl-heidelberg`` user.
To make it easier, put this information in your global ``~/.planemo.yml`` file. The format is described here: https://planemo.readthedocs.io/en/latest/configuration.html
The commands below work due to the ``.shed.yml`` file in this directory.
## Update testtoolshed
``planemo shed_update --shed_target testtoolshed``
Look at the result and then update the main toolshed.
## Update toolshed
``planemo shed_update``
......@@ -21,7 +21,7 @@
@barcode_len_cmd@
ADD=${ADD}
#if str($ADD) == "false":
BARCODE_RESULT_FILENAME=$BARCODE_RESULT_FILENAME
BARCODE_RESULT_FILENAME=${BARCODE_RESULT_FILENAME}
#end if
OF1=${OF1}
......@@ -54,10 +54,12 @@
</inputs>
<outputs>
<data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"/>
<data name="OF1" format_source="input_1" label="Je-Clipped {on_string}"/>
<data name="OF2" format_source="input_1" label="Je-Clipped {on_string}">
<filter>(type != "single")</filter>
<data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes">
<filter>!ADD</filter>
</data>
<data name="OF1" format_source="input_1" label="Je-Clip OF1: ${on_string}"/>
<data name="OF2" format_source="input_2" label="Je-Clip OF2: ${on_string}">
<filter>library["type"] != "single"</filter>
</data>
</outputs>
......
......@@ -17,8 +17,8 @@
<xml name="paired_options">
<when value="paired">
<param name="input_1" format="fastq" type="data" label="FASTQ file #1"/>
<param name="input_2" format="fastq" type="data" label="FASTQ file #2"/>
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/>
<param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/>
<yield />
<param name="SAME_HEADERS" type="boolean"
label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
......@@ -27,7 +27,7 @@
falsevalue="false" checked="false"/>
</when>
<when value="paired_collection">
<param name="input_1" format="fastq" type="data_collection" collection_type="paired"
<param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired"
label="FASTQ Paired Dataset"/>
<yield />
<param name="SAME_HEADERS" type="boolean"
......@@ -60,18 +60,18 @@
<option value="paired_collection">Paired-end Dataset Collection</option>
</param>
<when value="single">
<param name="input_1" format="fastq" type="data" label="FASTQ file"/>
<param name="I1" type="data" format="fastq" label="First Index File"/>
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
<param name="I1" type="data" format="fastq,gz" label="First Index File"/>
</when>
<expand macro="paired_options">
<param name="I1" type="data" format="fastq" label="First Index File"/>
<param name="I1" type="data" format="fastq,gz" label="First Index File"/>
<conditional name="I2_CONDITIONAL">
<param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
<option value="true">Yes</option>
<option value="false" selected="true">No</option>
</param>
<when value="true">
<param name="I2" type="data" format="fastq" label="Second Index File"/>
<param name="I2" type="data" format="fastq,gz" label="Second Index File"/>
<expand macro="bred_conditional"/>
</when>
<when value="false"/>
......@@ -88,7 +88,7 @@
<option value="paired_collection">Paired-end Dataset Collection</option>
</param>
<when value="single">
<param name="input_1" format="fastq" type="data" label="FASTQ file"/>
<param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
</when>
<expand macro="paired_options">
<yield />
......@@ -298,6 +298,8 @@ ${from_text_area}</configfile>
ZT=${ZT}
#if str( $RCHAR ) != "":
RCHAR=${RCHAR}
#else:
RCHAR=null
#end if
GZ=${GZ}
OUTPUT_DIR=results
......@@ -310,7 +312,7 @@ ${from_text_area}</configfile>
<param name="RCHAR" type="text"
label="Replace white space in the read name/header with speficied symbols (RCHAR)"
help="Set to empty for no replacement"
help="Set to empty or null for no replacement."
value=":"/>
<param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
......
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