Mercurial > repos > thanhlv > ariba

changeset 13:4b9cce1814a5 draft default tip

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"planemo upload for repository https://github.com/sanger-pathogens/ariba commit d340071e9db54a47286d2bc9aac490347b5c37ac-dirty"
author thanhlv
date Thu, 09 Sep 2021 09:42:44 +0000
parents 9944044da8a2
children
files ariba_run.xml
diffstat 1 files changed, 15 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/ariba_run.xml	Fri Oct 02 12:00:48 2020 +0000
+++ b/ariba_run.xml	Thu Sep 09 09:42:44 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="ariba_run" name="ARIBA run" version="@VERSION@">
+<tool id="ariba_run" name="ARIBA run" version="@VERSION@+galaxy1">
     <description>
         Runs the local assembly pipeline
     </description>
@@ -44,7 +44,8 @@
                 '$library.input1.reverse'
         #end if
 
-        out
+        out &&
+        if [ ! -e 'out/mlst_report.tsv' ] ; then touch out/mlst_report.tsv out/mlst_report.details.tsv ; fi
     ]]>    </command>
     <inputs>
         <conditional name="library">
@@ -113,13 +114,23 @@
         <data format="fasta" name="assemblies" label="${tool.name} on ${on_string}: gzipped FASTA file of the assemblies" from_work_dir="out/assemblies.fa.gz"/>
         <data format="gz" name="log_cluster" label="${tool.name} on ${on_string}: Log for the progress of each cluster" from_work_dir="out/log.clusters.gz"/>
         <data format="txt" name="tools_version" label="${tool.name} on ${on_string}: Tools version" from_work_dir="out/version_info.txt"/>
+        <data format="tabular" name="mlst_report" label="${tool.name} on ${on_string}: MLST report" from_work_dir="out/mlst_report.tsv">
+            <actions>
+                <action name="column_names" type="metadata" default="ST,adk,fumC,gyrB,icd,mdh,purA,recA" />
+            </actions>
+        </data>
+        <data format="tabular" name="mlst_detail_report" label="${tool.name} on ${on_string}: MLST detail report" from_work_dir="out/mlst_report.details.tsv">
+            <actions>
+                <action name="column_names" type="metadata" default="gene,allele,cov,pc,ctgs,depth,hetmin,hets" />
+            </actions>
+        </data>
     </outputs>
 
     <tests>
         <test>
             <param name="lib_type" value="paired"/>
-            <param name="R1" value="reads_1.fq" format="fastqsanger.gz"/>
-            <param name="R2" value="reads_2.fq" format="fastqsanger.gz" />
+            <param name="R1" value="reads_1.fq" ftype="fastqsanger.gz"/>
+            <param name="R2" value="reads_2.fq" ftype="fastqsanger.gz" />
             <param name="ariba_databases" value="PREPAREREF"/>
 
             <output name="report" file="OUT/report.tsv" ftype="tabular"/>