Mercurial > repos > shellac > sam_consensus_v3

diff sam-consensus-v3.xml @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam-consensus-v3.xml	Mon Mar 22 18:12:50 2021 +0000
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+<tool id="sam-consensus-v3" name="Sam consensus V3" version="0.2.8" python_template_version="3.5">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        perl '$__tool_directory__/call_consensus_from_sam_3.pl' '$samfile' 'fastafile' $mapq
+    ]]></command>
+    <inputs>
+        <param name="samfile" type="data" format="sam" label="SAM file"/>
+        <param name="fastafile" type="data" format="fasta" label="FASTA file"/>
+        <param name="mapq" type="integer" label="MAPQ" value="0"/>
+    </inputs>
+    <outputs>
+        <data name="scv3res" format="txt">
+            <discover_datasets pattern="__designation_and_ext__" directory="." visible="true"/>
+        </data>
+    </outputs>
+    <help><![CDATA[
+        Sam consensus v3 takes a sam file and a fasta file with a mapq parameter
+    ]]></help>
+</tool>
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