Mercurial > repos > iuc > porechop

diff porechop.xml @ 1:93d623d9979c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit 4155cc1e26dd6e647d882a550b5278141ab39314
author iuc
date Wed, 19 Sep 2018 08:35:02 -0400
parents 24822689acf8
children 5f76b20953e5
line wrap: on
line diff
--- a/porechop.xml	Tue Sep 18 16:24:49 2018 -0400
+++ b/porechop.xml	Wed Sep 19 08:35:02 2018 -0400
@@ -29,12 +29,12 @@
 
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fasta,fastq" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
-        <param name="format" type="select" label="Output format for the reads" help="Output format for the reads - if auto, the format will be chosen based on the output filename or the input read format">
-            <option selected="True" value="fasta">FASTA</option>
-            <option value="fastq">FASTQ</option>
-            <option value="fasta.gz">FASTA.gz</option>
-            <option value="fastq.gz">FASTQ.gz</option>
+        <param name="input_file" type="data" format="fasta,fastqsanger" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
+        <param name="format" type="select" label="Output format for the reads" help="Output format for the reads">
+            <option selected="True" value="fasta">fasta</option>
+            <option value="fastq">fastq</option>
+            <option value="fasta.gz">fasta.gz</option>
+            <option value="fastq.gz">fastq.gz</option>
         </param>
         <section name="barcode_binning_settings" title="Barcode binning settings">
             <param argument="--barcode_threshold" type="float" min="0" max="100" value="75.0" optional="True" label="Percent identity for binning"
@@ -84,9 +84,9 @@
     <outputs>
         <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed">
             <change_format>
-                <when input="format" value="fastq" format="fastq"/>
+                <when input="format" value="fastq" format="fastqsanger"/>
                 <when input="format" value="fasta.gz" format="fasta.gz"/>
-                <when input="format" value="fastq.gz" format="fastq.gz"/>
+                <when input="format" value="fastq.gz" format="fastqsanger.gz"/>
             </change_format>
         </data>
     </outputs>
@@ -99,7 +99,7 @@
         <test>
             <param name="input_file" ftype="fasta" value="test_format.fasta"/>
             <param name="format" value="fastq"/>
-            <output name="outfile" ftype="fastq" file="out.fastq"/>
+            <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
         </test>
         <test>
             <param name="input_file" ftype="fasta" value="test_format.fasta"/>
@@ -109,7 +109,7 @@
         <test>
             <param name="input_file" ftype="fasta" value="test_format.fasta"/>
             <param name="format" value="fastq.gz"/>
-            <output name="outfile" ftype="fastq.gz" file="out.fastq.gz" compare="sim_size"/>
+            <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/>
         </test>
         <test>
             <param name="input_file" ftype="fasta" value="test_format.fasta"/>