comparison macros.xml @ 10:d82339e37e8e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
author iuc
date Thu, 15 Aug 2019 01:54:13 -0400
parents d5659efd66aa
children 41929aa1e7f3
comparison
equal deleted inserted replaced
9:0a563fd2f22e 10:d82339e37e8e
1 <macros> 1 <macros>
2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
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
5 sync. -->
6 <!-- STAR version to be used -->
7 <token name="@VERSION@">2.7.2a</token>
8 <!-- STAR index version compatible with this version of STAR
9 This is the STAR version that introduced the index structure expected
10 by the current version.
11 It can be found for any specific version of STAR with:
12 STAR -h | grep versionGenome
13 or by looking for the versionGenome parameter in source/parametersDefault
14 of STAR's source code -->
15 <token name="@IDX_VERSION@">2.7.1a</token>
16
2 <xml name="requirements"> 17 <xml name="requirements">
3 <requirements> 18 <requirements>
4 <requirement type="package" version="2.6.0b">star</requirement> 19 <requirement type="package" version="@VERSION@">star</requirement>
5 <requirement type="package" version="1.8">samtools</requirement> 20 <requirement type="package" version="1.9">samtools</requirement>
6 </requirements> 21 </requirements>
7 </xml> 22 </xml>
23
24 <xml name="index_selection" token_with_gene_model="1">
25 <param argument="--genomeDir" name="genomeDir" type="select"
26 label="Select reference genome"
27 help="If your genome of interest is not listed, contact the Galaxy team">
28 <options from_data_table="rnastar_index2_versioned">
29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
30 <filter type="static_value" column="5" value="@IDX_VERSION@" />
31 <filter type="sort_by" column="2" />
32 <validator type="no_options" message="No indexes are available for the selected input dataset" />
33 </options>
34 </param>
35 </xml>
36
8 <token name="@FASTQ_GZ_OPTION@"> 37 <token name="@FASTQ_GZ_OPTION@">
9 --readFilesCommand zcat 38 --readFilesCommand zcat
10 </token> 39 </token>
11 <xml name="citations"> 40 <xml name="citations">
12 <citations> 41 <citations>
13 <citation type="doi">10.1093/bioinformatics/bts635</citation> 42 <citation type="doi">10.1093/bioinformatics/bts635</citation>
14 </citations> 43 </citations>
15 </xml> 44 </xml>
16 <xml name="@SJDBOPTIONS@"> 45 <xml name="@SJDBOPTIONS@" token_optional="true">
17 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/> 46 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
18 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> 47 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
19 </xml> 48 </xml>
20 <xml name="dbKeyActions"> 49 <xml name="dbKeyActions">
21 <actions> 50 <actions>
22 <conditional name="refGenomeSource.geneSource"> 51 <conditional name="refGenomeSource.geneSource">
23 <when value="indexed"> 52 <when value="indexed">
24 <action type="metadata" name="dbkey"> 53 <action type="metadata" name="dbkey">
25 <option type="from_data_table" name="rnastar_index2" column="1" offset="0"> 54 <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
26 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 55 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
27 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> 56 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
28 </option> 57 </option>
29 </action> 58 </action>
30 </when> 59 </when>
34 </action> 63 </action>
35 </when> 64 </when>
36 </conditional> 65 </conditional>
37 </actions> 66 </actions>
38 </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>
39 </macros> 163 </macros>