Mercurial > repos > dfornika > micall_lite

changeset 12:7747ba1a5557 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 20:01:26 -0400
parents 2f6edb60d16e
children 1c7832516ccd
files micall-lite.xml
diffstat 1 files changed, 13 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/micall-lite.xml	Fri Sep 20 19:42:28 2019 -0400
+++ b/micall-lite.xml	Fri Sep 20 20:01:26 2019 -0400
@@ -15,28 +15,25 @@
           micall
             '${input_pair.element_identifier}_R1.fastq.gz'
             '${input_pair.element_identifier}_R2.fastq.gz'
-          --outdir 'outdir'
+          --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}
         ]]>
     </command>
     <inputs>
         <param format="fastqsanger,fastqsanger.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
+        <param type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
     </inputs>
     <outputs>
-        <data name="align" format="tabular">
-            <discover_datasets directory="outdir" pattern="(?P&lt;designation&gt;.+)\.align\.csv" />
-        </data>
-        <data name="amino" format="tabular">
-            <discover_datasets directory="outdir" pattern="(?P&lt;designation&gt;.+)\.amino\.csv"/>
-        </data>
-        <data name="conseq" format="tabular">
-            <discover_datasets directory="outdir" pattern="(?P&lt;designation&gt;.+)\.conseq\.csv" />
-        </data>
-        <data name="insert" format="tabular">
-            <discover_datasets directory="outdir" pattern="(?P&lt;designation&gt;.+)\.insert\.csv" />
-        </data>
-        <data name="nuc" format="tabular">
-            <discover_datasets directory="outdir" pattern="(?P&lt;designation&gt;.+)\.nuc\.csv" />
-        </data>
+        <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" />
     </outputs>
     <tests>
         <test>