Commit 1553a880 authored by Mehmet Tekman's avatar Mehmet Tekman

output collections for galaxy

parent 25e8fd29
......@@ -74,6 +74,8 @@
<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"/>
......@@ -90,6 +92,34 @@
<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>
......
......@@ -290,6 +290,8 @@ ${from_text_area}</configfile>
falsevalue="false"
checked="true"
/>
<param name="COLLECT_OUTPUTS" type="boolean" label="Group forward and reverse reads into seperate collection outputs?" />
<section name="adv_options" title="Advanced Options" expanded="False">
<param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
truevalue="true" falsevalue="false" checked="false"
......@@ -333,14 +335,24 @@ ${from_text_area}</configfile>
<token name="@demultiplexer_common_outputs_cmd@">
METRICS_FILE_NAME=$METRICS_FILE_NAME
</token>
<xml name="demultiplexer_common_outputs">
<data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
<filter>COLLECT_OUTPUTS == 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"/>
</data>
<data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
<filter>(adv_options['DIAG'] == 'true')</filter>
</data>
<collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
<filter>COLLECT_OUTPUTS</filter>
<discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" />
</collection>
<collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
<filter>COLLECT_OUTPUTS</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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