Mercurial > repos > dfornika > mob_suite

changeset 46:9513a59a7364 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit c67e48b0706acad2d8d15783a779af07a67380e3-dirty"
author dfornika
date Thu, 21 Nov 2019 20:15:56 +0000
parents 4c5276f87370
children f286c91a0b92
files mob_hostrange.xml mob_recon.xml
diffstat 2 files changed, 16 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/mob_hostrange.xml	Thu Nov 14 01:40:58 2019 +0000
+++ b/mob_hostrange.xml	Thu Nov 21 20:15:56 2019 +0000
@@ -29,14 +29,14 @@
         ]]>
     </command>
     <inputs>
-        <param name="inputseq" type="data" format="fasta" optional="true" label="Input" help="plasmid FASTA file"/>
+        <param name="inputseq" type="data" format="fasta" label="Input plasmid" help="plasmid FASTA file"/>
         <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
         <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
         <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
-        <param name="replicon_name" type="text" optional="true"/>
-        <param name="relaxase_name" type="text" optional="true"/>
-        <param name="relaxase_accession" type="text" optional="true"/>
-        <param name="cluster_id" type="text" optional="true"/>
+        <param name="replicon_name" type="text" />
+        <param name="relaxase_name" type="text" />
+        <param name="relaxase_accession" type="text" />
+        <param name="cluster_id" type="text" />
     </inputs>
     <outputs>
         <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
--- a/mob_recon.xml	Thu Nov 14 01:40:58 2019 +0000
+++ b/mob_recon.xml	Thu Nov 21 20:15:56 2019 +0000
@@ -70,21 +70,21 @@
     <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
     <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome"/>
     <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
-            <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
+      <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
     </collection>
   </outputs>
   <tests>
     <test>
-        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
-        <section name="adv_param">
-         <param name="unicycler_contigs" value="True"/>
-         <param name="run_circlator"  value="True"/>
-        </section>
-        <output name="contig_report">
-          <assert_contents>
-            <has_text text="NC_019097"/>
-          </assert_contents>  
-        </output> 
+      <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
+      <section name="adv_param">
+        <param name="unicycler_contigs" value="True"/>
+        <param name="run_circlator"  value="True"/>
+      </section>
+      <output name="contig_report">
+        <assert_contents>
+          <has_text text="NC_019097"/>
+        </assert_contents>
+      </output>
     </test>
   </tests>
   <help>