Mercurial > repos > dfornika > match_plasmid_to_reference

diff match_plasmid_to_reference.xml @ 4:826ddf832bef draft default tip

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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 13:52:40 -0500
parents d56b4f743779
children
line wrap: on
line diff
--- a/match_plasmid_to_reference.xml	Wed Nov 06 01:20:36 2019 -0500
+++ b/match_plasmid_to_reference.xml	Wed Nov 06 13:52:40 2019 -0500
@@ -5,8 +5,12 @@
     <command detect_errors="exit_code"><![CDATA[
         '$__tool_directory__/match_plasmid_to_reference.py'
         --plasmid '${plasmid}'
-        --reference_plasmids
-        #for $reference_plasmid in $reference_plasmids:
+        --reference_plasmids_genbank
+        #for $reference_plasmid in $reference_plasmids_genbank:
+          '${reference_plasmid}'
+        #end for
+        --reference_plasmids_fasta
+        #for $reference_plasmid in $reference_plasmids_fasta:
           '${reference_plasmid}'
         #end for
         --mob_typer_report '${concatenated_mob_typer_reports}'
@@ -14,26 +18,35 @@
     ]]></command>
     <inputs>
         <param name="plasmid" type="data" format="fasta" />
-        <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
+        <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" />
+	<param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" />
         <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
     </inputs>
     <outputs>
         <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
-        <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid" format="genbank"/>
+        <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/>
+	<data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/>
 	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
     </outputs>
     <tests>
         <test>
             <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
-            <param name="reference_plasmids">
+            <param name="reference_plasmids_genbank">
                 <collection type="list">
                     <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
                     <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
                 </collection>
             </param>
+            <param name="reference_plasmids_fasta">
+                <collection type="list">
+                    <element name="CP008719" value="CP008719.fa" ftype="fasta" />
+                    <element name="JQ739157" value="JQ739157.fa" ftype="fasta" />
+                </collection>
+            </param>
             <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
             <output name="output_plasmid" file="outdir/plasmid.fasta" />
-            <output name="matched_reference_plasmid" file="outdir/reference_plasmid.gbk" />
+            <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
+            <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
             <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
         </test>
     </tests>