diff lumpyexpress.xml @ 0:e5150e64206a draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lumpyexpress.xml	Tue Oct 16 15:55:49 2018 -0400
@@ -0,0 +1,74 @@
+<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.0">
+    <description>Single or paired end SV detection</description>
+
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="0.8.3">pysam</requirement>
+        <requirement type="package" version="1.13.1">numpy</requirement>
+        <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="0.1.24">samblaster</requirement>
+        <requirement type="package" version="0.6.5">sambamba</requirement>
+        <requirement type="package" version="4.2.1">gawk</requirement>
+    </requirements>
+
+    <version_command>___COMMAND___ ___VERSION_FLAG___</version_command>
+
+    <command detect_errors="aggressive">
+        <![CDATA[
+            $__tool_directory__/lumpy_wrapper.tcsh
+            '$paired'
+            '$outfile'
+            #for $bam in $bams
+                '$bam'
+            #end for
+        ]]>
+    </command>
+
+    <inputs>
+        <param format="bam"
+               name="bams"
+               label="Bam file(s)"
+               argument="argument positions 3-N"
+
+               type="data"
+               multiple="true"
+
+               help="Optionally sorted/indexed whole bam files.  Splitters and discordants will be extracted from this file."/>
+
+        <param name="paired"
+               label="Bam files contain paired end data"
+               argument="argument position 1"
+
+               type="boolean"
+               truevalue="1"
+               falsevalue="0"
+               checked="no"
+               value="false"/>
+    </inputs>
+
+    <outputs>
+        <data format="vcf" name="outfile" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="bams" value="test1-1.bam,test1-2.bam,test1-3.bam"/>
+            <param name="paired" value="1"/>
+            <output name="outfile" file="lumpy-test1.vcf"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            Paired-end data is processed with lumpyexpress using only the required arguments.  Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`.  Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools
+
+            Split reads and discordant reads are extracted from the supplied bam files.  Each bam file should represent a different sample.
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
+    </citations>
+
+</tool>