# HG changeset patch
# User devteam
# Date 1485784166 18000
# Node ID 53646aaaafefb9ecaea0f654605ff933512628fd
# Parent  bd3a1e0de84cff07210b260c2849f6a5f4396a6e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea

diff -r bd3a1e0de84c -r 53646aaaafef bwa-mem.xml
--- a/bwa-mem.xml	Fri Dec 30 08:11:12 2016 -0500
+++ b/bwa-mem.xml	Mon Jan 30 08:49:26 2017 -0500
@@ -114,8 +114,8 @@
         <option value="paired_iv">Paired Interleaved</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"/>
         <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
@@ -123,10 +123,10 @@
         </param>
       </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"/>
       </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"/>
         <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
@@ -134,7 +134,7 @@
         </param>
       </when>
       <when value="paired_iv">
-        <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
         <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
@@ -261,6 +261,15 @@
     <test>
       <param name="reference_source_selector" value="history" />
       <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+      <param name="fastq_input_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-mem-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="index_a" value="is"/>
       <param name="fastq_input_selector" value="paired"/>
       <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
diff -r bd3a1e0de84c -r 53646aaaafef bwa.xml
--- 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"/>
diff -r bd3a1e0de84c -r 53646aaaafef test-data/bwa-mem-fastq1.fq.gz
Binary file test-data/bwa-mem-fastq1.fq.gz has changed