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comparison yaha.xml @ 2:37cac55c1081 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 41b852cad408786bc7049f3c002f85d1aebda063-dirty
author mvdbeek
date Tue, 03 Jan 2017 05:02:28 -0500
parents 584220a3c520
children bcba667aef5b
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1:584220a3c520 2:37cac55c1081
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 #if $reference_genome.reference_genome_source == "history" or "reference": 12 #if $reference_genome.reference_genome_source == "history" or "reference":
13 #if $reference_genome.reference_genome_source == "history": 13 #if $reference_genome.reference_genome_source == "history":
14 ln -f -s "$reference_genome.history_item" genome.fa && 14 ln -f -s "$reference_genome.history_item" genome.fa &&
15 #elif $reference_genome.reference_genome_source == "reference": 15 #elif $reference_genome.reference_genome_source == "reference":
16 ln -f -s "$reference_genome.fasta_item" genome.fa && 16 ln -f -s "$reference_genome.fasta_item.fields.path" genome.fa &&
17 #end if 17 #end if
18 yaha -g genome.fa -H $reference_genome.maxHitsIndex -L $reference_genome.wordLenIndex -S $reference_genome.skipDistanceIndex && 18 yaha -g genome.fa -H $reference_genome.maxHitsIndex -L $reference_genome.wordLenIndex -S $reference_genome.skipDistanceIndex &&
19 #set maxHitsIndex = "%s%s" % ("0" * (5 - len(str($reference_genome.maxHitsIndex))), $reference_genome.maxHitsIndex) 19 #set maxHitsIndex = "%s%s" % ("0" * (5 - len(str($reference_genome.maxHitsIndex))), $reference_genome.maxHitsIndex)
20 #set skipdist = $reference_genome.skipDistanceIndex if len(str($reference_genome.skipDistanceIndex)) > 1 else "0%s" % $reference_genome.skipDistanceIndex 20 #set skipdist = $reference_genome.skipDistanceIndex if len(str($reference_genome.skipDistanceIndex)) > 1 else "0%s" % $reference_genome.skipDistanceIndex
21 #set wordLenIndex = $reference_genome.wordLenIndex if len(str($reference_genome.wordLenIndex)) > 1 else "0%s" % $reference_genome.wordLenIndex 21 #set wordLenIndex = $reference_genome.wordLenIndex if len(str($reference_genome.wordLenIndex)) > 1 else "0%s" % $reference_genome.wordLenIndex