Mercurial > repos > iuc > data_manager_star_index_builder

comparison data_manager/macros.xml @ 7:9a231bb19a3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
author iuc
date Thu, 15 Aug 2019 11:28:53 -0400
parents 54cddd903437
children d2f4bfcf269a
comparison
equal deleted inserted replaced
6:54cddd903437 7:9a231bb19a3b
2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager 2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
3 whenever you make changes to the following two version tokens! 3 whenever you make changes to the following two version tokens!
4 The data manager uses a symlink to this macro file to keep the versions in 4 The data manager uses a symlink to this macro file to keep the versions in
5 sync. --> 5 sync. -->
6 <!-- STAR version to be used --> 6 <!-- STAR version to be used -->
7 <token name="@VERSION@">2.7.1a</token> 7 <token name="@VERSION@">2.7.2a</token>
8 <!-- STAR index version compatible with this version of STAR 8 <!-- STAR index version compatible with this version of STAR
9 This is the STAR version that introduced the index structure expected 9 This is the STAR version that introduced the index structure expected
10 by the current version. 10 by the current version.
11 It can be found for any specific version of STAR with: 11 It can be found for any specific version of STAR with:
12 STAR -h | grep versionGenome 12 STAR -h | grep versionGenome
63 </action> 63 </action>
64 </when> 64 </when>
65 </conditional> 65 </conditional>
66 </actions> 66 </actions>
67 </xml> 67 </xml>
68 <token name="@TEMPINDEX@"><![CDATA[
69 ## Create temporary index for custom reference
70 #if str($refGenomeSource.geneSource) == 'history':
71 mkdir -p tempstargenomedir &&
72 STAR
73 --runMode genomeGenerate
74 --genomeDir 'tempstargenomedir'
75 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
76 ## Handle difference between indices with/without annotations
77 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
78 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
79 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
80 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
81 --sjdbGTFtagExonParentTranscript Parent
82 #end if
83 #end if
84 #if str($refGenomeSource.genomeSAindexNbases):
85 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
86 #end if
87 --runThreadN \${GALAXY_SLOTS:-4}
88 &&
89 #end if
90 ]]></token>
91 <token name="@REFGENOMEHANDLING" ><![CDATA[
92 --runThreadN \${GALAXY_SLOTS:-4}
93 --genomeLoad NoSharedMemory
94 --genomeDir
95 #if str($refGenomeSource.geneSource) == 'history':
96 tempstargenomedir
97 #else:
98 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
99 ## Handle difference between indices with/without annotations
100 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
101 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
102 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
103 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
104 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
105 --sjdbGTFtagExonParentTranscript Parent
106 #end if
107 #end if
108 #end if
109 #end if
110 ]]></token>
111 <xml name="stdio" >
112 <stdio>
113 <regex match="FATAL 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"/>
116 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
117 </stdio>
118 </xml>
119 <xml name="refgenomehandling" >
120 <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 <option value="indexed" selected="true">Use a built-in index</option>
123 <option value="history">Use reference genome from history and create temporary index</option>
124 </param>
125 <when value="indexed">
126 <conditional name="GTFconditional">
127 <param name="GTFselect" type="select"
128 label="Reference genome with or without an annotation"
129 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
130 <option value="without-gtf">use genome reference with builtin gene-model</option>
131 <option value="with-gtf">use genome reference without builtin gene-model</option>
132 </param>
133 <when value="with-gtf">
134 <expand macro="index_selection" with_gene_model="0" />
135 <expand macro="@SJDBOPTIONS@" />
136 </when>
137 <when value="without-gtf">
138 <expand macro="index_selection" with_gene_model="1" />
139 </when>
140 </conditional>
141 </when>
142 <when value="history">
143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
144 <!-- Currently, this parameter is not exposed in the wrapper,
145 but used only in the tests to avoid excessive index sizes for
146 the tiny test genomes. -->
147 <param name="genomeSAindexNbases" type="hidden" value="" />
148 <conditional name="GTFconditional">
149 <param name="GTFselect" type="select"
150 label="Build index with our without known splice junctions annotation"
151 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
152 <option value="without-gtf">build index without gene-model</option>
153 <option value="with-gtf">build index with gene-model</option>
154 </param>
155 <when value="with-gtf">
156 <expand macro="@SJDBOPTIONS@" optional="false"/>
157 </when>
158 <when value="without-gtf" />
159 </conditional>
160 </when>
161 </conditional>
162 </xml>
68 </macros> 163 </macros>