# HG changeset patch
# User dpryan79
# Date 1473796895 14400
# Node ID f9c8c79b8b087797a5e141d8cd502bc73c4ea6a7
# Parent  24b3fdf9c32fe65741149c6246ca2fd150dc1a1b
Uploaded

diff -r 24b3fdf9c32f -r f9c8c79b8b08 bwameth.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwameth.xml	Tue Sep 13 16:01:35 2016 -0400
@@ -0,0 +1,93 @@
+<tool id="bwameth" name="bwameth" version="0.20">
+  <description>Fast and accurate aligner of BS-Seq reads.</description>
+  <requirements>
+    <requirement type="package" version="0.20">toolshed</requirement>
+    <requirement type="package" version="1.2">samtools</requirement>
+    <requirement type="package" version="0.7.12">bwa</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+    <regex match="Error:" />
+    <regex match="Exception:" />
+    <regex match="Exception :" />
+  </stdio>
+  <version_command>bwameth.py --version</version_command>
+  <command interpreter="python">
+<![CDATA[
+    bwameth_wrapper.py 
+        -p "\${GALAXY_SLOTS:-4}"
+
+    #if $referenceSource.source != "indexed":
+        --makeIndex $referenceSource.reference
+    #else
+        --premadeIndex $referenceSource.index.fields.path
+    #end if
+
+    #if str($readGroup).strip() != "":
+        --readGroup "${readGroup}"
+    #end if
+
+    #if $single_or_paired.single_or_paired_opts == 'single':
+        $single_or_paired.input_singles
+    #else:
+        $single_or_paired.input_mate1 $single_or_paired.input_mate2
+    #end if
+]]>
+  </command>
+  <inputs>
+    <conditional name="referenceSource">
+      <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
+        <option value="history" selected="True">Use one from the history</option>
+        <option value="indexed">Use a built-in index</option>
+      </param>
+      <when value="history">
+        <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" />
+      </when>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
+          <options from_data_table="bwameth_indexes">
+            <filter type="sort_by" column="2"/>
+              <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </param>
+      </when>
+    </conditional>
+
+    <conditional name="single_or_paired">
+      <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="input_singles" type="data" format="fastq" label="FASTQ" help="FASTQ file." />
+      </when>
+      <when value="paired">
+        <param name="input_mate1" type="data" format="fastq" label="First read in pair" help="FASTQ file." />
+        <param name="input_mate2" type="data" format="fastq" label="Second read in pair" help="FASTQ file." />
+      </when>
+    </conditional>
+    <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'" />
+  </inputs>
+  <outputs>
+    <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="referenceSource" value="history" />
+      <param name="reference" value="ref.fa" />
+      <param name="single_or_paired_opts" value="paired" />
+      <param name="input_mate1" value="t_R1.fastq.gz" />
+      <param name="input_mate2" value="t_R2.fastq.gz" />
+      <output file="alignments.bam" ftype="bam" name="output" />
+    </test>
+  </tests>
+  <help>
+<![CDATA[
+
+**What it does**
+
+BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
+]]>
+  </help>
+</tool>