diff cpo_predictions.xml @ 0:917a05a03ac9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpo_predictions.xml	Tue Aug 14 17:18:49 2018 -0400
@@ -0,0 +1,60 @@
+<tool id="cpo_prediction_galaxy" name="cpoParser" version="0.1.0">
+	<description>this tool parses stuff</description>
+	<requirements>
+		<requirement type="package" version="0.23.4">pandas</requirement>
+		<requirement type="package" version="3.6">python</requirement>
+	</requirements>
+	<command detect_errors="exit_code">
+    <![CDATA[
+	    python '$__tool_directory__/galaxy_prediction.py'
+		'-i $ID'
+		'-m $mlst'
+		'-c $mobsuitecontig'
+		'-f $mobsuiteaggregate'
+		'-a $abricate'
+		'-r $rgi'
+		'-e $expected'
+		'-s $__tool_directory__/scheme_species_map.tab'
+    ]]>
+	</command>
+    <inputs>
+        <param type="text" name="ID"/>
+        <param type="data" name="mlst" format="tabular" />
+        <param type="data" name="mobsuitecontig" format="tabular" />
+        <param type="data" name="mobsuiteaggregate" format="tabular" />
+        <param type="data" name="abricate" format="tabular" />
+        <param type="data" name="rgi" format="tabular" />
+        <param type="text" name="expected"/>
+    </inputs>
+    <outputs>
+        <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
+		<data name="txtSummary" format="text" from_work_dir="summary.txt"/>
+    </outputs>
+	<tests>
+        <test>
+            <param name="ID" value="BC11-Kpn005_S2"/>
+            <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
+            <param name="mobsuitecontig" value="contig_report"/>
+            <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
+            <param name="abricate" value="BC11-Kpn005_S2.cp"/>
+            <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
+            <param name="expected" value="Klebsiella pneumoniae"/>
+            <output name="tsvSummary" file="summary.tsv"/>
+			<output name="txtSummary" file="summary.txt"/>
+        </test>
+    </tests>
+	<help>
+		This tool parses stuff.
+	</help>
+	<citations>
+        <citation type="bibtex">
+@misc{cpo,
+  author = {j, j},
+  year = {2018},
+  title = {cpo_prediction},
+  publisher = {j},
+  journal = {j of j},
+  url = {https://bfjia.net,
+}</citation>
+    </citations>
+</tool>