Mercurial > repos > iuc > snippy

diff snippy.xml @ 12:fa016f1eea1a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
author iuc
date Wed, 07 Apr 2021 11:24:48 +0000
parents 5bbf9eada9c2
children
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--- a/snippy.xml	Wed Mar 11 03:50:47 2020 -0400
+++ b/snippy.xml	Wed Apr 07 11:24:48 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@">
+<tool id="snippy" name="snippy" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
     </description>
@@ -69,17 +69,17 @@
                 <option value="paired_iv">Paired Interleaved</option>
             </param>
             <when value="paired">
-                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
-                <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
+                <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="single">
-                <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                <param name="fastq_input_single" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
             <when value="paired_collection">
-                <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <param name="fastq_input" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_iv">
-                <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+                <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
             </when>
         </conditional>
 
@@ -148,8 +148,8 @@
                 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
             </conditional>
             <param name="fastq_input_selector" value="paired" />
-            <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
-            <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
+            <param name="fastq_input1" ftype="fastqsanger.gz" value="a_1.fastq.gz" />
+            <param name="fastq_input2" ftype="fastqsanger.gz" value="a_2.fastq.gz" />
             <param name="mincov" value="2" />
             <param name="minqual" value="60" />
             <param name="outputs" value="outgff,outsum" />