diff data_manager/bwameth_index_builder.xml @ 0:a7fb84abef45 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwameth_index_builder.xml	Tue Nov 22 17:12:00 2016 -0500
@@ -0,0 +1,59 @@
+<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.7.12">bwa</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="0.2.0">bwameth</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        #if str($sequence_id).strip() != "":
+            #set $dbkey = $sequence_id
+        #else:
+            #set $dbkey = $all_fasta_source.fields.dbkey
+        #end if
+
+        #if str($sequence_name).strip() != "":
+            #set $name = $sequence_name
+        #else:
+            #set $name = $all_fasta_source.fields.name
+        #end if
+
+        python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" 
+            --fasta_filename "${all_fasta_source.fields.path}" 
+            --dbkey "${dbkey}"
+            --name "${name}" 
+            --data_table_name "bwameth_indexes"
+        ]]>
+    </command>
+    <inputs>
+        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
+            <options from_data_table="all_fasta" />
+        </param>
+        <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/>
+        <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/>
+    </inputs>
+    <outputs>
+        <data format="data_manager_json" name="out_file" />
+    </outputs>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+What is BWA-meth?
+-----------------
+
+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>