--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwameth.xml	Wed Sep 14 16:55:47 2016 -0400
@@ -0,0 +1,118 @@
+<tool id="bwameth" name="bwameth" version="0.2.0">
+    <description>Fast and accurate aligner of BS-Seq reads.</description>
+    <requirements>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="0.2.0">bwameth</requirement>
+    </requirements>
+    <version_command>bwameth.py --version</version_command>
+    <command detect_errors="aggressive">
+<![CDATA[
+    #if $referenceSource.source != "indexed":
+        mkdir index_dir &&
+        ln -s '$referenceSource.reference' index_dir/genome.fa &&
+        bwameth.py index index_dir/genome.fa &&
+        #set index="index_dir/genome.fa"
+    #else
+        #set index=$referenceSource.index.fields.path
+    #end if
+
+    bwameth.py
+        -t "\${GALAXY_SLOTS:-4}"
+        --reference "${index}"
+
+    #if str($readGroup).strip() != "":
+        --read-group "${readGroup}"
+    #end if
+
+    #if $single_or_paired.single_or_paired_opts == 'single':
+        $single_or_paired.input_singles
+    #elif $single_or_paired.single_or_paired_opts == 'paired':
+        $single_or_paired.input_mate1 $single_or_paired.input_mate2
+    #else:
+        $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse
+    #end if
+    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam -
+]]>
+    </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>
+                <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." />
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." />
+            </when>
+            <when value="paired_collection">
+                <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
+            </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'">
+            <sanitizer sanitize="False"/>
+        </param>
+    </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.gz" />
+            <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="output.bam" ftype="bam" name="output" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="referenceSource" value="history" />
+            <param name="reference" value="ref.fa.gz" />
+            <param name="single_or_paired_opts" value="paired_collection" />
+            <param name="input_mate1">
+                <collection type="paired">
+                    <element name="forward" value="t_R1.fastq.gz" />
+                    <element name="reverse" value="t_R2.fastq.gz" />
+                </collection>
+            </param>
+            <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
+        </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>
+    <citations>
+        <citation type="bibtex">@misc{1401.1129,
+        Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
+        Title = {Fast and accurate alignment of long bisulfite-seq reads},
+        Year = {2014},
+        Eprint = {arXiv:1401.1129},
+        }</citation>
+    </citations>
+</tool>

Binary file test-data/output.bam has changed

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwameth_indexes.loc.sample	Wed Sep 14 16:55:47 2016 -0400
@@ -0,0 +1,10 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of bwa-meth indices, using three columns tab separated:
+#
+# bwameth_index_id\tSome description text\t/path/to/genome.fasta
+#
+# An index can be created with the following command:
+#
+# bwameth.py index /some/path/genome.fa
+#
+# "/some/path/genome.fa" would then be the last column in the line

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Sep 14 16:55:47 2016 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="bwameth_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/bwameth_indexes.loc" />
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 14 16:55:47 2016 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+       <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bwameth" version="0.2.0">
+       <repository changeset_revision="54d14a994f71" name="package_python_2_7_bwameth_0_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>