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diff bwa.xml @ 14:051eba708f43 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
author devteam
date Thu, 01 Jun 2017 11:38:47 -0400
parents 53646aaaafef
children 48f306c57611
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--- a/bwa.xml	Mon Jan 30 08:49:26 2017 -0500
+++ b/bwa.xml	Thu Jun 01 11:38:47 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="@VERSION@.1">
+<tool id="bwa" name="Map with BWA" version="@VERSION@.2">
   <description>- map short reads (&lt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -233,8 +233,8 @@
         <option value="single_bam">Single BAM</option>
       </param>
       <when value="paired">
-        <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"/>
+        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
+        <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
         <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,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
+        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
         <conditional name="adv_se_options">
 
           <expand macro="advanced_se_options" />
@@ -322,6 +322,14 @@
     <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="single"/>
+      <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
+      <param name="analysis_type_selector" value="illumina"/>
+      <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.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"/>
       <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
       <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>