Mercurial > repos > mvdbeek > wtdbg2

changeset 1:fe60b4299555 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
author mvdbeek
date Mon, 26 Nov 2018 09:10:05 -0500
parents 7bb3cf8b9a5d
children 79430547460a
files wtdbg2.xml
diffstat 1 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/wtdbg2.xml	Mon Nov 26 07:51:32 2018 -0500
+++ b/wtdbg2.xml	Mon Nov 26 09:10:05 2018 -0500
@@ -12,7 +12,7 @@
 wtdbg2 -t \${GALAXY_SLOTS:-1} 
 -i '$inputs' 
 -fo prefix 
-#if $preset
+#if $preset.select_preset != 'manual'
     -x '$preset.select_preset'
 #else 
     -k $preset.kmer_length
@@ -40,19 +40,19 @@
         <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" help="Select input reads"/>
         <conditional name="preset">
             <param name="select_preset" type="select">
-                <option value="rsII/rs">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option>
-                <option value="sequel/sq">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option>
-                <option value="nanopore/ont">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option>
-                <option value="corrected/ccs">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option>
+                <option value="rsII">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option>
+                <option value="sequel">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option>
+                <option value="nanopore">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option>
+                <option value="corrected">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option>
                 <option value="manual">Specify Options</option>
             </param>
-            <when value="rsII/rs">
+            <when value="rsII">
             </when>
-            <when value="sequel/sq">
+            <when value="sequel">
             </when>
-            <when value="nanopore/ont">
+            <when value="nanopore">
             </when>
-            <when value="corrected/ccs">
+            <when value="corrected">
             </when>
             <when value="manual">
                 <param name="kmer_length" argument="-k" type="integer" value="0" min="0" max="25" label="kmer fsize"/>
@@ -80,7 +80,7 @@
     <tests>
         <test>
             <param name="inputs" value="ecoli-reads.fasta" ftype="fasta"/>
-            <param name="preset|select_preset" value="rsII/rs"/>
+            <param name="preset|select_preset" value="rsII"/>
             <output name="contigs" value="contigs.txt"/>
             <output name="consensus" value="consensus.fa"/>
             <output name="polished_consensus" value="polished_consensus.fa"/>