Mercurial > repos > rdvelazquez > bioext_bam2msa

diff bam2msa.xml @ 0:72b7678b5b09 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
author rdvelazquez
date Wed, 14 Mar 2018 14:46:48 -0400
parents
children c7c46222ee0c
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam2msa.xml	Wed Mar 14 14:46:48 2018 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
+    <description>to FASTA multiple sequence alignment</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+    bam2msa
+        #if $region_start and $region_end:
+            -r $region_start:$region_end
+        #end if
+        $input $output
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bam,sam" label="Input BAM file" />
+        <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences" />
+        <param name="region_end" type="integer" value="0" optional="True" label="End coordinate" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="bam" value="bealign-out1.bam" />
+            <output name="output" file="bam2msa-out1.fa" />
+        </test>
+        <test>
+            <param name="input" ftype="bam" value="bealign-out2.bam" />
+            <output name="output" file="bam2msa-out2.fa" />
+        </test>
+    </tests>
+    <help>Extract MSA from a BAM file</help>
+    <expand macro="citations" />
+</tool>