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comparison data_manager/macros.xml @ 7:6c6c6df09e64 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 a8e319862d723654c372a6d71e5de76e052586a9"
author iuc
date Wed, 05 Aug 2020 09:38:12 -0400
parents 64deddb6a8ec
children c520a52b5174
comparison
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6:64deddb6a8ec 7:6c6c6df09e64
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 STAR and 4 The data manager uses a symlink to this macro file to keep the STAR and
5 the index versions in sync, but you should manually adjust the +galaxy 5 the index versions in sync, but you should manually adjust the +galaxy
6 version number. --> 6 version number. -->
7 <!-- STAR version to be used --> 7 <!-- STAR version to be used -->
8 <token name="@VERSION@">2.7.2b</token> 8 <token name="@VERSION@">2.7.5b</token>
9 <!-- STAR index version compatible with this version of STAR 9 <!-- STAR index version compatible with this version of STAR
10 This is the STAR version that introduced the index structure expected 10 This is the STAR version that introduced the index structure expected
11 by the current version. 11 by the current version.
12 It can be found for any specific version of STAR with: 12 It can be found for any specific version of STAR with:
13 STAR -h | grep versionGenome 13 STAR -h | grep versionGenome
14 or by looking for the versionGenome parameter in source/parametersDefault 14 or by looking for the versionGenome parameter in source/parametersDefault
15 of STAR's source code --> 15 of STAR's source code -->
16 <token name="@IDX_VERSION@">2.7.1a</token> 16 <token name="@IDX_VERSION@">2.7.4a</token>
17 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
17 18
18 <xml name="requirements"> 19 <xml name="requirements">
19 <requirements> 20 <requirements>
20 <requirement type="package" version="@VERSION@">star</requirement> 21 <requirement type="package" version="@VERSION@">star</requirement>
21 <requirement type="package" version="1.9">samtools</requirement> 22 <requirement type="package" version="1.9">samtools</requirement>
25 26
26 <xml name="index_selection" token_with_gene_model="0"> 27 <xml name="index_selection" token_with_gene_model="0">
27 <param argument="--genomeDir" name="genomeDir" type="select" 28 <param argument="--genomeDir" name="genomeDir" type="select"
28 label="Select reference genome" 29 label="Select reference genome"
29 help="If your genome of interest is not listed, contact the Galaxy team"> 30 help="If your genome of interest is not listed, contact the Galaxy team">
30 <options from_data_table="rnastar_index2_versioned"> 31 <options from_data_table="@IDX_DATA_TABLE@">
31 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> 32 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
32 <filter type="static_value" column="5" value="@IDX_VERSION@" /> 33 <filter type="static_value" column="5" value="@IDX_VERSION@" />
33 <filter type="sort_by" column="2" /> 34 <filter type="sort_by" column="2" />
34 <validator type="no_options" message="No indexes are available for the selected input dataset" /> 35 <validator type="no_options" message="No indexes are available for the selected input dataset" />
35 </options> 36 </options>
51 <xml name="dbKeyActions"> 52 <xml name="dbKeyActions">
52 <actions> 53 <actions>
53 <conditional name="refGenomeSource.geneSource"> 54 <conditional name="refGenomeSource.geneSource">
54 <when value="indexed"> 55 <when value="indexed">
55 <action type="metadata" name="dbkey"> 56 <action type="metadata" name="dbkey">
56 <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0"> 57 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
57 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 58 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
58 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> 59 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
59 </option> 60 </option>
60 </action> 61 </action>
61 </when> 62 </when>
74 STAR 75 STAR
75 --runMode genomeGenerate 76 --runMode genomeGenerate
76 --genomeDir 'tempstargenomedir' 77 --genomeDir 'tempstargenomedir'
77 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' 78 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
78 ## Handle difference between indices with/without annotations 79 ## Handle difference between indices with/without annotations
79 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 80 #if 'GTFconditional' in $refGenomeSource:
80 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' 81 ## GTFconditional exists only in STAR, but not STARsolo
81 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 82 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
82 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 83 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
84 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
85 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
86 --sjdbGTFtagExonParentTranscript Parent
87 #end if
88 #end if
89 #else:
90 ## ref genome selection is less complex for STARsolo cause
91 ## with-gtf is mandatory there
92 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
93 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
94 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
83 --sjdbGTFtagExonParentTranscript Parent 95 --sjdbGTFtagExonParentTranscript Parent
84 #end if 96 #end if
85 #end if 97 #end if
86 #if str($refGenomeSource.genomeSAindexNbases): 98 #if str($refGenomeSource.genomeSAindexNbases):
87 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} 99 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
108 #end if 120 #end if
109 #end if 121 #end if
110 #end if 122 #end if
111 #end if 123 #end if
112 ]]></token> 124 ]]></token>
125 <xml name="ref_selection">
126 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
127 <!-- Currently, this parameter is not exposed in the wrapper,
128 but used only in the tests to avoid excessive index sizes for
129 the tiny test genomes. -->
130 <param name="genomeSAindexNbases" type="hidden" value="" />
131 </xml>
113 <xml name="stdio" > 132 <xml name="stdio" >
114 <stdio> 133 <stdio>
115 <regex match="FATAL error" source="both" level="fatal"/> 134 <regex match="FATAL error" source="both" level="fatal"/>
116 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> 135 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
117 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> 136 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
118 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> 137 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
119 <yield /> 138 <yield />
120 </stdio> 139 </stdio>
121 </xml> 140 </xml>
122 <xml name="refgenomehandling" >
123 <conditional name="refGenomeSource">
124 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
125 <option value="indexed" selected="true">Use a built-in index</option>
126 <option value="history">Use reference genome from history and create temporary index</option>
127 </param>
128 <when value="indexed">
129 <conditional name="GTFconditional">
130 <param name="GTFselect" type="select"
131 label="Reference genome with or without an annotation"
132 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.">
133 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
134 <option value="with-gtf">use genome reference with builtin gene-model</option>
135 </param>
136 <when value="with-gtf">
137 <expand macro="index_selection" with_gene_model="1" />
138 </when>
139 <when value="without-gtf">
140 <expand macro="index_selection" with_gene_model="0" />
141 <expand macro="@SJDBOPTIONS@" />
142 </when>
143 </conditional>
144 </when>
145 <when value="history">
146 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
147 <!-- Currently, this parameter is not exposed in the wrapper,
148 but used only in the tests to avoid excessive index sizes for
149 the tiny test genomes. -->
150 <param name="genomeSAindexNbases" type="hidden" value="" />
151 <conditional name="GTFconditional">
152 <param name="GTFselect" type="select"
153 label="Build index with our without known splice junctions annotation"
154 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.">
155 <option value="without-gtf">build index without gene-model</option>
156 <option value="with-gtf">build index with gene-model</option>
157 </param>
158 <when value="with-gtf">
159 <expand macro="@SJDBOPTIONS@" optional="false"/>
160 </when>
161 <when value="without-gtf" />
162 </conditional>
163 </when>
164 </conditional>
165 </xml>
166 </macros> 141 </macros>