Mercurial > repos > dfornika > micall_lite

changeset 14:79d9866da30f draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
author dfornika
date Fri, 20 Sep 2019 20:17:28 -0400
parents 1c7832516ccd
children 61667ff2c8b5
files micall-lite.xml
diffstat 1 files changed, 6 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/micall-lite.xml	Fri Sep 20 20:02:17 2019 -0400
+++ b/micall-lite.xml	Fri Sep 20 20:17:28 2019 -0400
@@ -16,12 +16,7 @@
             '${input_pair.element_identifier}_R1.fastq.gz'
             '${input_pair.element_identifier}_R2.fastq.gz'
           --readlen ${readlen}
-          --outdir 'outdir' &&
-          mv outdir/*.align.csv ${align} &&
-          mv outdir/*.amino.csv ${amino} &&
-          mv outdir/*.conseq.csv ${conseq} &&
-          mv outdir/*.insert.csv ${insert} &&
-          mv outdir/*.nuc.csv ${nuc}
+          --outdir 'outdir'
         ]]>
     </command>
     <inputs>
@@ -29,11 +24,11 @@
         <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
     </inputs>
     <outputs>
-        <data name="align" format="tabular" />
-        <data name="amino" format="tabular" />
-        <data name="conseq" format="tabular" />
-        <data name="insert" format="tabular" />
-        <data name="nuc" format="tabular" />
+        <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
+        <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
+        <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
+        <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
+        <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
     </outputs>
     <tests>
         <test>