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diff bwa.xml @ 13:53646aaaafef draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea
author devteam
date Mon, 30 Jan 2017 08:49:26 -0500
parents bd3a1e0de84c
children 051eba708f43
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line diff
--- a/bwa.xml	Fri Dec 30 08:11:12 2016 -0500
+++ b/bwa.xml	Mon Jan 30 08:49:26 2017 -0500
@@ -233,8 +233,8 @@
         <option value="single_bam">Single BAM</option>
       </param>
       <when value="paired">
-        <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
-        <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
+        <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
         <conditional name="adv_pe_options">
 
           <expand macro="advanced_pe_options" />
@@ -243,7 +243,7 @@
       </when>
 
       <when value="paired_collection">
-        <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+        <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
         <conditional name="adv_pe_options">
 
           <expand macro="advanced_pe_options" />
@@ -252,7 +252,7 @@
       </when>
 
       <when value="single">
-        <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
+        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
         <conditional name="adv_se_options">
 
           <expand macro="advanced_se_options" />
@@ -331,6 +331,15 @@
     <test>
       <param name="reference_source_selector" value="history" />
       <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+      <param name="input_type_selector" value="paired"/>
+      <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
+      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+      <param name="analysis_type_selector" value="illumina"/>
+      <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
+    </test>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
       <param name="input_type_selector" value="paired_bam"/>
       <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
       <param name="analysis_type_selector" value="illumina"/>