Mercurial > repos > rnateam > segemehl

diff segemehl.xml @ 7:be1a3cc2cf45 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit b193689f9f30ce65a77be2d2c00929e3335a7d82
author bgruening
date Wed, 26 Jul 2017 15:25:28 -0400
parents c6cef240817e
children 90b8941e5115
line wrap: on
line diff
--- a/segemehl.xml	Wed Jul 26 10:14:42 2017 -0400
+++ b/segemehl.xml	Wed Jul 26 15:25:28 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="segemehl" name="segemehl" version="0.2.0.2">
+<tool id="segemehl" name="segemehl" version="0.2.0.3">
   <description>short read mapping with gaps</description>
   <requirements>
     <requirement type="package" version="0.2.0">segemehl</requirement>
@@ -72,12 +72,12 @@
         #if $maxout:
             --maxout $maxout
         #end if
-        #if str( $splitreads.splits ) == "--split":
+        #if str( $splitreads.splits ) == "splits":
             --splits
-            --minsplicecover $minsplicecover
-            --minfragscore $minfragscore
-            --minfraglen $minfraglen
-            --splicescorescale $splicescorescale
+            --minsplicecover $splitreads.minsplicecover
+            --minfragscore $splitreads.minfragscore
+            --minfraglen $splitreads.minfraglen
+            --splicescorescale $splitreads.splicescorescale
         #end if
         -M $maxinterval
         -E $evalue
@@ -131,9 +131,9 @@
     <conditional name="splitreads">
       <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)">
         <option value="nosplit">No splits</option>
-        <option value="--splits">Split reads</option>
+        <option value="splits">Split reads</option>
       </param>
-      <when value="--splits">
+      <when value="splits">
         <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
         <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
         <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
@@ -172,9 +172,18 @@
       <param name="own_reference_genome" value="chr1.fa" />
       <param name="library" value="single" />
       <param name="input_query" value="test.fastq" />   
-      <param name="splits" value="true" />
+      <param name="splits" value="nosplit" />
       <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
     </test>
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="own_reference_genome" value="chr1.fa" />
+      <param name="library" value="single" />
+      <param name="input_query" value="test.fastq" />   
+      <param name="splits" value="splits" />
+	  <param name="minsplicecover" value="40" />
+      <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
+    </test>
   </tests>
   <help>
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