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Commit 8adb16fc authored by Jelle Scholtalbers's avatar Jelle Scholtalbers
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Merge branch 'mtekman-master'

parents 25e8fd29 02cddee5
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src/galaxy/je-demultiplex-illu.xml
View file @ 8adb16fc
......@@ -95,7 +95,8 @@
<param name="MMD" value="2"/>
<param name="Q" value="20"/>
<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_2" file="illu_unassigned_2_PE.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.
Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
......
src/galaxy/je-demultiplex.xml
View file @ 8adb16fc
......@@ -60,7 +60,8 @@
<param name="type" value="single"/>
<param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
<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" />
</output>
</test>
......@@ -74,10 +75,12 @@
<param name="BM" value="BOTH"/>
<param name="BRED" value="false"/>
<param name="COLLECT_OUTPUTS" value="false" />
<param name="barcode_list_type_con" value="text"/>
<param name="barcode_text"
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_2" file="unassigned_2_PE.txt" />
<discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/>
......@@ -90,6 +93,33 @@
<discovered_dataset designation="sample1_CACTGTGTATAG_1" file="sample1_CACTGTGTATAG_1.txt"/>
</output>
</test>
<test>
<!-- Repeat of previous but with collection outputs -->
<param name="type" value="paired"/>
<param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
<param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/>
<param name="BPOS" value="BOTH"/>
<param name="BM" value="BOTH"/>
<param name="BRED" value="false"/>
<param name="barcode_list_type_con" value="text"/>
<param name="barcode_text"
value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
<param name="COLLECT_OUTPUTS" value="true" />
<output_collection name="COLLECTION_1" type="list">
<element name="sample1_CACTGTGTATAG_1.txt" value="sample4_CGAAACCACTGT_1.txt"/>
<element name="sample3_GCTACCTGGTCA_1.txt" value="sample3_GCTACCTGGTCA_1.txt"/>
<element name="sample2_ATTCCGTCCGTC_1.txt" value="sample2_ATTCCGTCCGTC_1.txt"/>
<element name="sample1_CACTGTGTATAG_1.txt" value="sample1_CACTGTGTATAG_1.txt"/>
</output_collection>
<output_collection name="COLLECTION_2" type="list">
<element name="sample4_CGAAACCACTGT_2.txt" value="sample4_CGAAACCACTGT_2.txt"/>
<element name="sample3_GCTACCTGGTCA_2.txt" value="sample3_GCTACCTGGTCA_2.txt"/>
<element name="sample2_ATTCCGTCCGTC_2.txt" value="sample2_ATTCCGTCCGTC_2.txt"/>
<element name="sample1_CACTGTGTATAG_2.txt" value="sample1_CACTGTGTATAG_2.txt"/>
</output_collection>
</test>
</tests>
<help>
......@@ -103,6 +133,7 @@ Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
......
src/galaxy/macros.xml
View file @ 8adb16fc
<macros>
<token name="@VERSION_STRING@">1.2</token>
<token name="@VERSION_STRING@">1.2.1</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="1.2">je-suite</requirement>
......@@ -278,19 +278,19 @@ ${from_text_area}</configfile>
</xml>
<token name="@demultiplexer_common_output_options_cmd@">
KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
STATS_ONLY=${adv_options.STATS_ONLY}
#if str( $adv_options.DIAG ) == "true":
KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ}
STATS_ONLY=${STATS_ONLY}
#if str( $DIAG ) == "true":
BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
#end if
</token>
<xml name="demultiplexer_common_output_options">
<param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truevalue="true"
falsevalue="false"
checked="true"
/>
<section name="adv_options" title="Advanced Options" expanded="False">
<!--<section name="output_options" title="Output Options" expanded="True">-->
<param name="COLLECT_OUTPUTS" type="boolean"
truevalue="true" falsevalue="false" checked="false"
label="Output forward and reverse reads in dataset collections" />
<param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truevalue="true" falsevalue="false" checked="true"/>
<param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
truevalue="true" falsevalue="false" checked="false"
help="This file will
......@@ -300,7 +300,7 @@ ${from_text_area}</configfile>
<param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
truevalue="true" falsevalue="false" checked="false"
help="do not demultiplex." />
</section>
<!--</section>-->
</xml>
<token name="@common_options_cmd@">
......@@ -333,14 +333,24 @@ ${from_text_area}</configfile>
<token name="@demultiplexer_common_outputs_cmd@">
METRICS_FILE_NAME=$METRICS_FILE_NAME
</token>
<xml name="demultiplexer_common_outputs">
<data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
<!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"-->
<data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true">
<filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter>
<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
</data>
<data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/>
<data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
<filter>(adv_options['DIAG'] == 'true')</filter>
<filter>DIAG</filter>
</data>
<collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
<filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
<discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" />
</collection>
<collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
<filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
<discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsangar" directory="results" visible="false" />
</collection>
</xml>
<xml name="citations">
<citations>
......
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