Mercurial > repos > dfornika > mob_suite

changeset 25:728003387137 draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty
author dfornika
date Mon, 23 Sep 2019 20:42:43 -0400
parents 4a2918d96c96
children 4b9f7624a255
files mob_recon.xml
diffstat 1 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/mob_recon.xml	Mon Sep 23 20:27:22 2019 -0400
+++ b/mob_recon.xml	Mon Sep 23 20:42:43 2019 -0400
@@ -27,10 +27,11 @@
     --min_con_evalue '${adv_param.min_con_evalue}'
     --min_rep_ident '${adv_param.min_rep_ident}'
     --min_mob_ident '${adv_param.min_mob_ident}'
-    --min_con_ident  '${adv_param.min_con_ident}'
-    --min_rpp_ident   '${adv_param.min_rpp_ident}'
+    --min_con_ident '${adv_param.min_con_ident}'
+    --min_rpp_ident '${adv_param.min_rpp_ident}'
     --outdir '.' && 
-    mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true)
+    mkdir ./plasmids && (cp plasmid*.fasta ./plasmids 2> /dev/null || true) &&
+    tar -cvzf "plasmids.tar.gz" plasmids
   ]]>  
   </command>
   <inputs>
@@ -65,12 +66,11 @@
     </section>  
   </inputs>
   <outputs>
-    <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
-    <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
-    <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
-    <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))">
-            <discover_datasets pattern="__name_and_ext__" directory="sequences" />
-    </collection>
+    <data name="contig_report" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
+    <data name="repetitive_element_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
+    <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
+    <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name} on ${on_string}: Chromosomal contigs" />
+    <data name="plasmids" format="tar.gz" from_work_dir="plasmids.tar.gz" label="${tool.name} on ${on_string}: Chromosomal contigs" />
   </outputs>
   <tests>
     <test>
@@ -79,7 +79,7 @@
          <param name="unicycler_contigs" value="True"/>
          <param name="run_circlator"  value="True"/>
         </section>
-        <output name="outfile1">
+        <output name="contig_report">
           <assert_contents>
             <has_text text="NC_019097"/>
           </assert_contents>