Mercurial > repos > jdv > porechop

changeset 9:e3ad639c692a draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 83364d7d78ca5524a08065daef995bfcd54a379d-dirty
author jdv
date Fri, 01 Dec 2017 21:27:15 -0500
parents 852b3fe95c20
children 0cb1ba651e9e
files porechop.xml
diffstat 1 files changed, 19 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/porechop.xml	Fri Oct 20 23:11:21 2017 -0400
+++ b/porechop.xml	Fri Dec 01 21:27:15 2017 -0500
@@ -133,12 +133,24 @@
 
         <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
             <filter>out_format == 'fastq'</filter>
+            <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
             <discover_datasets pattern="__designation_and_ext__" directory="out" format="fastqsanger" />
         </collection>
         <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
             <filter>out_format == 'fasta'</filter>
+            <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
             <discover_datasets pattern="__designation_and_ext__" directory="out" format="fasta" />
         </collection>
+        <data format="fastq" name="ouput_fastq">
+              <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fastq" visible="true" assign_primary_output="true" />
+            <filter>out_format == 'fastq'</filter>
+            <filter>demux_section['demux_options']['demux'] == 'no'</filter>
+        </data>
+        <data format="fasta" name="ouput_fasta">
+              <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fasta" visible="true" assign_primary_output="true" />
+            <filter>out_format == 'fasta'</filter>
+            <filter>demux_section['demux_options']['demux'] == 'no'</filter>
+        </data>
 
         <data format="tabular" name="result_table" label="${tool.name} on ${on_string} (summary)" /> 
     </outputs>
@@ -178,6 +190,13 @@
                 <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
             </output_collection>
         </test>
+        <test>
+            <param name="input" value="test_barcodes.fastq" ftype="fastq" />
+            <param name="demux" value="no" />
+            <param name="trim" value="yes" />
+            <param name="out_format" value="fasta" />
+            <output name="output_fasta" file="no_demux.fasta" compare="diff" />
+        </test>
     </tests>
 
     <!-- ***************************************************************** -->