Commit 02cddee5 authored by Jelle Scholtalbers's avatar Jelle Scholtalbers

remove section and better handle different outputs

parent 1553a880
...@@ -95,7 +95,8 @@ ...@@ -95,7 +95,8 @@
<param name="MMD" value="2"/> <param name="MMD" value="2"/>
<param name="Q" value="20"/> <param name="Q" value="20"/>
<param name="DIAG" value="false"/> <param name="DIAG" value="false"/>
<output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"> <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"/>
<output name="DEMULTIPLEX_RESULTS" ftype="tabular">
<discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" /> <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
<discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" /> <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
<discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/> <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/>
...@@ -123,6 +124,7 @@ Input files are fastq files, and can be in gzip compressed format. ...@@ -123,6 +124,7 @@ Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de). Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------ ------
......
...@@ -60,7 +60,8 @@ ...@@ -60,7 +60,8 @@
<param name="type" value="single"/> <param name="type" value="single"/>
<param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
<param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/> <param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/>
<output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"> <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"/>
<output name="DEMULTIPLEX_RESULTS" ftype="tabular">
<discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" /> <discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" />
</output> </output>
</test> </test>
...@@ -75,11 +76,11 @@ ...@@ -75,11 +76,11 @@
<param name="BRED" value="false"/> <param name="BRED" value="false"/>
<param name="COLLECT_OUTPUTS" value="false" /> <param name="COLLECT_OUTPUTS" value="false" />
<param name="barcode_list_type_con" value="text"/> <param name="barcode_list_type_con" value="text"/>
<param name="barcode_text" <param name="barcode_text"
value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/> value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
<output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"> <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"/>
<output name="DEMULTIPLEX_RESULTS" ftype="tabular">
<discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" /> <discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" />
<discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" /> <discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" />
<discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/> <discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/>
...@@ -101,7 +102,6 @@ ...@@ -101,7 +102,6 @@
<param name="BPOS" value="BOTH"/> <param name="BPOS" value="BOTH"/>
<param name="BM" value="BOTH"/> <param name="BM" value="BOTH"/>
<param name="BRED" value="false"/> <param name="BRED" value="false"/>
<param name="barcode_list_type_con" value="text"/> <param name="barcode_list_type_con" value="text"/>
<param name="barcode_text" <param name="barcode_text"
value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/> value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
...@@ -133,6 +133,7 @@ Input files are fastq files, and can be in gzip compressed format. ...@@ -133,6 +133,7 @@ Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de). Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------ ------
......
<macros> <macros>
<token name="@VERSION_STRING@">1.2</token> <token name="@VERSION_STRING@">1.2.1</token>
<xml name="requirements"> <xml name="requirements">
<requirements> <requirements>
<requirement type="package" version="1.2">je-suite</requirement> <requirement type="package" version="1.2">je-suite</requirement>
...@@ -278,21 +278,19 @@ ${from_text_area}</configfile> ...@@ -278,21 +278,19 @@ ${from_text_area}</configfile>
</xml> </xml>
<token name="@demultiplexer_common_output_options_cmd@"> <token name="@demultiplexer_common_output_options_cmd@">
KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ}
STATS_ONLY=${adv_options.STATS_ONLY} STATS_ONLY=${STATS_ONLY}
#if str( $adv_options.DIAG ) == "true": #if str( $DIAG ) == "true":
BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
#end if #end if
</token> </token>
<xml name="demultiplexer_common_output_options"> <xml name="demultiplexer_common_output_options">
<param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" <!--<section name="output_options" title="Output Options" expanded="True">-->
truevalue="true" <param name="COLLECT_OUTPUTS" type="boolean"
falsevalue="false" truevalue="true" falsevalue="false" checked="false"
checked="true" label="Output forward and reverse reads in dataset collections" />
/> <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
<param name="COLLECT_OUTPUTS" type="boolean" label="Group forward and reverse reads into seperate collection outputs?" /> truevalue="true" falsevalue="false" checked="true"/>
<section name="adv_options" title="Advanced Options" expanded="False">
<param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)" <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
truevalue="true" falsevalue="false" checked="false" truevalue="true" falsevalue="false" checked="false"
help="This file will help="This file will
...@@ -302,7 +300,7 @@ ${from_text_area}</configfile> ...@@ -302,7 +300,7 @@ ${from_text_area}</configfile>
<param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)" <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
truevalue="true" falsevalue="false" checked="false" truevalue="true" falsevalue="false" checked="false"
help="do not demultiplex." /> help="do not demultiplex." />
</section> <!--</section>-->
</xml> </xml>
<token name="@common_options_cmd@"> <token name="@common_options_cmd@">
...@@ -335,22 +333,22 @@ ${from_text_area}</configfile> ...@@ -335,22 +333,22 @@ ${from_text_area}</configfile>
<token name="@demultiplexer_common_outputs_cmd@"> <token name="@demultiplexer_common_outputs_cmd@">
METRICS_FILE_NAME=$METRICS_FILE_NAME METRICS_FILE_NAME=$METRICS_FILE_NAME
</token> </token>
<xml name="demultiplexer_common_outputs"> <xml name="demultiplexer_common_outputs">
<data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result"> <data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true">
<filter>COLLECT_OUTPUTS == False</filter> <filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter>
<!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"-->
<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/> <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
</data> </data>
<data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/>
<data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics"> <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
<filter>(adv_options['DIAG'] == 'true')</filter> <filter>DIAG</filter>
</data> </data>
<collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" > <collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
<filter>COLLECT_OUTPUTS</filter> <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
<discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" /> <discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" />
</collection> </collection>
<collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" > <collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
<filter>COLLECT_OUTPUTS</filter> <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
<discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsangar" directory="results" visible="false" /> <discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsangar" directory="results" visible="false" />
</collection> </collection>
</xml> </xml>
......
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