Mercurial > repos > dfornika > match_plasmid_to_reference

diff match_plasmid_to_reference.xml @ 0:8bb674372911 draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:08:43 -0500
parents
children 3616b6eda1da
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match_plasmid_to_reference.xml	Wed Nov 06 00:08:43 2019 -0500
@@ -0,0 +1,31 @@
+<tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
+    <description>Pick plasmids containing specific genes</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '$__tool_directory__/match_plasmid_to_reference.py'
+        --plasmid '${plasmid}'
+        --reference_plasmids
+        #for $reference_plasmid in $reference_plasmids:
+          '${reference_plasmid}'
+        #end for
+        --concatenated_mob_typer_reports '${concatenated_mob_typer_reports}'
+        --outdir outdir
+    ]]></command>
+    <inputs>
+        <param name="plasmid" type="data" format="fasta" />
+        <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
+        <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
+    </inputs>
+    <outputs>
+        <data name="plasmid" from_work_dir="outdir/plasmid.fasta" />
+        <data name="reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
+	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>