Mercurial > repos > iuc > rgrnastar

comparison macros.xml @ 12:39bde80cd248 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
author iuc
date Tue, 27 Aug 2019 05:58:33 -0400
parents 41929aa1e7f3
children 850f3679b9b4
comparison
equal deleted inserted replaced
11:41929aa1e7f3 12:39bde80cd248
86 #end if 86 #end if
87 --runThreadN \${GALAXY_SLOTS:-4} 87 --runThreadN \${GALAXY_SLOTS:-4}
88 && 88 &&
89 #end if 89 #end if
90 ]]></token> 90 ]]></token>
91 <token name="@REFGENOMEHANDLING" ><![CDATA[ 91 <token name="@REFGENOMEHANDLING@" ><![CDATA[
92 --runThreadN \${GALAXY_SLOTS:-4} 92 --runThreadN \${GALAXY_SLOTS:-4}
93 --genomeLoad NoSharedMemory 93 --genomeLoad NoSharedMemory
94 --genomeDir 94 --genomeDir
95 #if str($refGenomeSource.geneSource) == 'history': 95 #if str($refGenomeSource.geneSource) == 'history':
96 tempstargenomedir 96 tempstargenomedir
97 #else: 97 #else:
98 '${refGenomeSource.GTFconditional.genomeDir.fields.path}' 98 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
99 ## Handle difference between indices with/without annotations 99 ## Handle difference between indices with/without annotations
100 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 100 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
101 #if $refGenomeSource.GTFconditional.sjdbGTFfile: 101 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
102 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang 102 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
103 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 103 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
104 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 104 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
105 --sjdbGTFtagExonParentTranscript Parent 105 --sjdbGTFtagExonParentTranscript Parent
112 <stdio> 112 <stdio>
113 <regex match="FATAL error" source="both" level="fatal"/> 113 <regex match="FATAL error" source="both" level="fatal"/>
114 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> 114 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
115 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> 115 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
116 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> 116 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
117 <yield />
117 </stdio> 118 </stdio>
118 </xml> 119 </xml>
119 <xml name="refgenomehandling" > 120 <xml name="refgenomehandling" >
120 <conditional name="refGenomeSource"> 121 <conditional name="refGenomeSource">
121 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options"> 122 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
130 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> 131 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
131 <option value="with-gtf">use genome reference with builtin gene-model</option> 132 <option value="with-gtf">use genome reference with builtin gene-model</option>
132 </param> 133 </param>
133 <when value="with-gtf"> 134 <when value="with-gtf">
134 <expand macro="index_selection" with_gene_model="1" /> 135 <expand macro="index_selection" with_gene_model="1" />
135 <expand macro="@SJDBOPTIONS@" />
136 </when> 136 </when>
137 <when value="without-gtf"> 137 <when value="without-gtf">
138 <expand macro="index_selection" with_gene_model="0" /> 138 <expand macro="index_selection" with_gene_model="0" />
139 <expand macro="@SJDBOPTIONS@" />
139 </when> 140 </when>
140 </conditional> 141 </conditional>
141 </when> 142 </when>
142 <when value="history"> 143 <when value="history">
143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> 144 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />