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comparison rg_rnaStar.xml @ 3:318b2a9d54dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
author iuc
date Fri, 21 Apr 2017 07:58:59 -0400
parents ace9f5a2b40f
children 99b17b74a8cd
comparison
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2:ace9f5a2b40f 3:318b2a9d54dd
1 <tool id="rna_star" name="RNA STAR" version="2.4.0d-2"> 1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="2.4.0d">rnastar</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements"/>
7
7 <stdio> 8 <stdio>
9 <regex match="FATAL error" source="both" level="fatal"/>
8 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> 10 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
9 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> 11 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
10 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> 12 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
11 <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
12 </stdio> 13 </stdio>
13 14
15 <!--
16 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):
17 Hi Gary,
18
19 if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.
20 If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.
21
22 Cheers
23 Alex
24 -->
14 <command><![CDATA[ 25 <command><![CDATA[
15 ## Create temporary index for custom reference 26 ## Create temporary index for custom reference
16 #if str($refGenomeSource.genomeSource) == 'history': 27 #if str($refGenomeSource.geneSource) == 'history':
17 mkdir -p tempstargenomedir && 28 mkdir -p tempstargenomedir &&
18 STAR 29 STAR
19 --runMode genomeGenerate 30 --runMode genomeGenerate
20 --genomeDir "tempstargenomedir" 31 --genomeDir 'tempstargenomedir'
21 --genomeFastaFiles "$refGenomeSource.ownFile" 32 --genomeFastaFiles '$refGenomeSource.genomeFastaFiles'
33 #if $refGenomeSource.sjdbGTFfile:
34 --sjdbGTFfile '$refGenomeSource.sjdbGTFfile'
35 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
36 #end if
22 --runThreadN \${GALAXY_SLOTS:-4} 37 --runThreadN \${GALAXY_SLOTS:-4}
38 &&
39 #end if
40
41 STAR
42 --runThreadN \${GALAXY_SLOTS:-4}
43 --genomeLoad NoSharedMemory
44 --genomeDir
45 #if str($refGenomeSource.geneSource) == 'history':
46 'tempstargenomedir'
47 #if $refGenomeSource.sjdbGTFfile:
48 --sjdbGTFfile '$refGenomeSource.sjdbGTFfile'
49 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
50 #end if
51 #else
52 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
53 #end if
54
55 --readFilesIn
56 #if str($singlePaired.sPaired) == "paired_collection"
57 '$singlePaired.input.forward' '$singlePaired.input.reverse'
58
59 #if $singlePaired.input.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
60 @FASTQ_GZ_OPTION@
61 #end if
62 #else
63 '$singlePaired.input1'
64 #if str($singlePaired.sPaired) == "paired"
65 '$singlePaired.input2'
66 #end if
67
68 #if $singlePaired.input1.is_of_type("fastq.gz", "fastqsanger.gz"):
69 @FASTQ_GZ_OPTION@
70 #end if
71 #end if
72
73 --outSAMtype BAM SortedByCoordinate
74
75 ## Handle difference between indices with/without annotations
76 #if str($refGenomeSource.geneSource) == 'indexed':
77 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
78 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
79 --sjdbOverhang '$refGenomeSource.GTFconditional.sjdbOverhang'
80 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
81 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
82 --sjdbGTFtagExonParentTranscript Parent
83 #end if
84 #end if
85 #end if
86 #end if
87
88 #if $quantMode:
89 --quantMode GeneCounts
90 #end if
91
92 ## Output parameters
93 #if str( $output_params.output_select ) == "yes":
94 --outSAMattributes $output_params.outSAMattributes
95 --outSAMstrandField $output_params.outSAMstrandField
96 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
97 #if str( $output_params.output_params2.output_select2 ) == "yes":
98 --outSAMunmapped $output_params.output_params2.outSAMunmapped
99 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
100 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique"
101 --outFilterType $output_params.output_params2.outFilterType
102 --outFilterMultimapScoreRange "$output_params.output_params2.outFilterMultimapScoreRange"
103 --outFilterMultimapNmax "$output_params.output_params2.outFilterMultimapNmax"
104 --outFilterMismatchNmax "$output_params.output_params2.outFilterMismatchNmax"
105 --outFilterMismatchNoverLmax "$output_params.output_params2.outFilterMismatchNoverLmax"
106 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax"
107 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin"
108 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
109 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
110 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
111 #end if
112 #end if
113
114 ## Other parameters
115 #if str( $params.settingsType ) == "star_fusion":
116 ## Preset parameters for STAR-Fusion
117 --outReadsUnmapped None
118 --chimSegmentMin 12
119 --chimJunctionOverhangMin 12
120 --alignSJDBoverhangMin 10
121 --alignMatesGapMax 200000
122 --alignIntronMax 200000
123
124 ## --twopass1readsN 100000000
125 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
126 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
127
128 #elif str( $params.settingsType ) == "full":
129 ## Extended parameter options
130
131 ## Seed parameter options
132 --seedSearchStartLmax "$params.seed.seedSearchStartLmax"
133 --seedSearchStartLmaxOverLread "$params.seed.seedSearchStartLmaxOverLread"
134 --seedSearchLmax "$params.seed.seedSearchLmax"
135 --seedMultimapNmax "$params.seed.seedMultimapNmax"
136 --seedPerReadNmax "$params.seed.seedPerReadNmax"
137 --seedPerWindowNmax "$params.seed.seedPerWindowNmax"
138 --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow"
23 139
24 #if str($refGenomeSource.geneModel) != 'None': 140 ## Alignment parameter options
25 --sjdbOverhang "$refGenomeSource.overhang" 141 --alignIntronMin "$params.align.alignIntronMin"
26 --sjdbGTFfile "$refGenomeSource.geneModel" 142 --alignIntronMax "$params.align.alignIntronMax"
27 143 --alignMatesGapMax "$params.align.alignMatesGapMax"
28 #if str($refGenomeSource.geneModel.ext) == 'gff3': 144 --alignSJoverhangMin "$params.align.alignSJoverhangMin"
29 --sjdbGTFtagExonParentTranscript Parent 145 --alignSJDBoverhangMin "$params.align.alignSJDBoverhangMin"
146 --alignSplicedMateMapLmin "$params.align.alignSplicedMateMapLmin"
147 --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
148 --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
149 --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
150 --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
151 --alignEndsType $params.align.alignEndsType
152
153 ## Chimeric alignment parameter options
154 #if str( $params.chim.chim_select ) == "yes":
155 --chimSegmentMin "$params.chim.chimSegmentMin"
156 --chimScoreMin "$params.chim.chimScoreMin"
157 --chimScoreDropMax "$params.chim.chimScoreDropMax"
158 --chimScoreSeparation "$params.chim.chimScoreSeparation"
159 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
160 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
30 #end if 161 #end if
31 #end if 162 #end if
32 ; 163
33 #end if
34
35
36 ## Actual alignment
37 STAR
38 --runThreadN \${GALAXY_SLOTS:-4}
39 --genomeLoad NoSharedMemory
40 #if str($refGenomeSource.genomeSource) == 'history':
41 --genomeDir "tempstargenomedir"
42 #else
43 --genomeDir "$refGenomeSource.index.fields.path"
44 #end if
45
46 --readFilesIn
47 #if str($singlePaired.sPaired) == "paired_collection"
48 "$singlePaired.input.forward" "$singlePaired.input.reverse"
49 #else
50 "$singlePaired.input1"
51 #if str($singlePaired.sPaired) == "paired"
52 "$singlePaired.input2"
53 #end if
54 #end if
55
56 ## Output parameters
57 #if str( $output_params.output_select ) == "yes":
58 --outSAMattributes $output_params.outSAMattributes
59 --outSAMstrandField $output_params.outSAMstrandField
60 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
61 #if str( $output_params.output_params2.output_select2 ) == "yes":
62 --outSAMunmapped $output_params.output_params2.unmapped_opt
63 --outSAMprimaryFlag $output_params.output_params2.primary_opt
64 --outSAMmapqUnique "$output_params.output_params2.unique"
65 --outFilterType $output_params.output_params2.sjfilter_opt
66 --outFilterMultimapScoreRange "$output_params.output_params2.multiScoreRange"
67 --outFilterMultimapNmax "$output_params.output_params2.multiNmax"
68 --outFilterMismatchNmax "$output_params.output_params2.mismatchNmax"
69 --outFilterMismatchNoverLmax "$output_params.output_params2.mismatchNoverLmax"
70 --outFilterMismatchNoverReadLmax "$output_params.output_params2.mismatchNoverReadLmax"
71 --outFilterScoreMin "$output_params.output_params2.scoreMin"
72 --outFilterScoreMinOverLread "$output_params.output_params2.scoreMinOverLread"
73 --outFilterMatchNmin "$output_params.output_params2.matchNmin"
74 --outFilterMatchNminOverLread "$output_params.output_params2.matchNminOverLread"
75 #end if
76 #end if
77
78 ## Other parameters
79 #if str( $params.settingsType ) == "star_fusion":
80 ## Preset parameters for STAR-Fusion
81 ## --twopass1readsN 100000000
82 ## --sjdbOverhang 100
83 --outReadsUnmapped None
84 --chimSegmentMin 12
85 --chimJunctionOverhangMin 12
86 --alignSJDBoverhangMin 10
87 --alignMatesGapMax 200000
88 --alignIntronMax 200000
89 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
90 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
91
92 #elif str( $params.settingsType ) == "full":
93 ## Extended parameter options
94
95 ## Seed parameter options
96 #if str( $params.seed.seed_select ) == "yes":
97 --seedSearchStartLmax "$params.seed.searchStart"
98 --seedSearchStartLmaxOverLread "$params.seed.searchStartNorm"
99 --seedSearchLmax "$params.seed.searchLmax"
100 --seedMultimapNmax "$params.seed.multimap"
101 --seedPerReadNmax "$params.seed.readMax"
102 --seedPerWindowNmax "$params.seed.windowMax"
103 --seedNoneLociPerWindow "$params.seed.oneSeed"
104 #end if
105
106 ## Alignment parameter options
107 #if str( $params.align.align_select ) == "yes":
108 --alignIntronMin "$params.align.intronMin"
109 --alignIntronMax "$params.align.intronMax"
110 --alignMatesGapMax "$params.align.gapMax"
111 --alignSJoverhangMin "$params.align.sjOverhang"
112 --alignSJDBoverhangMin "$params.align.sjdbOverhang"
113 --alignSplicedMateMapLmin "$params.align.splicedMate"
114 --alignSplicedMateMapLminOverLmate "$params.align.splicedMateNorm"
115 --alignWindowsPerReadNmax "$params.align.windows"
116 --alignTranscriptsPerWindowNmax "$params.align.transWindow"
117 --alignTranscriptsPerReadNmax "$params.align.transRead"
118 --alignEndsType $params.align.endsType_opt
119 #end if
120
121 ## Chimeric alignment parameter options
122 #if str( $params.chim.chim_select ) == "yes":
123 --chimSegmentMin "$params.chim.segmentMin"
124 --chimScoreMin "$params.chim.scoreMin"
125 --chimScoreDropMax "$params.chim.scoreDrop"
126 --chimScoreSeparation "$params.chim.scoreSep"
127 --chimScoreJunctionNonGTAG "$params.chim.scoreJunction"
128 --chimJunctionOverhangMin "$params.chim.junctionOverhang"
129 #end if
130
131 #end if
132
133 ## BAM conversion.
134
135 ## Convert aligned reads.
136 && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Aligned.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - AlignedSorted 2>/dev/null
137
138 ## Convert chimeric reads. 164 ## Convert chimeric reads.
139 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.segmentMin) > 0 ): 165 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
140 && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Chimeric.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - ChimericSorted 2>/dev/null 166 &&
167 samtools view
168 -@ \${GALAXY_SLOTS:-4}
169 -Shb Chimeric.out.sam |
170
171 samtools sort
172 -@ \${GALAXY_SLOTS:-4} - ChimericSorted
141 #end if 173 #end if
142 ]]></command> 174 ]]></command>
143 175
144 <inputs> 176 <inputs>
145 <!-- FASTQ input(s) and options specifically for paired-end data. --> 177 <!-- FASTQ input(s) and options specifically for paired-end data. -->
146 <conditional name="singlePaired"> 178 <conditional name="singlePaired">
147 <param name="sPaired" type="select" label="Single-end or paired-end reads"> 179 <param name="sPaired" type="select" label="Single-end or paired-end reads">
148 <option value="single" selected="true">Single-end</option> 180 <option value="single" selected="true">Single-end</option>
149 <option value="paired">Paired-end (as individual datasets)</option> 181 <option value="paired">Paired-end (as individual datasets)</option>
150 <option value="paired_collection">Paired-end (as collection)</option> 182 <option value="paired_collection">Paired-end (as collection)</option>
151 </param> 183 </param>
152 <when value="single"> 184 <when value="single">
153 <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/> 185 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
154 </when> 186 </when>
155 <when value="paired"> 187 <when value="paired">
156 <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/> 188 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
157 <param format="fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/> 189 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
158 </when> 190 </when>
159 <when value="paired_collection"> 191 <when value="paired_collection">
160 <param format="fastq,fasta" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/> 192 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
161 </when> 193 </when>
162 </conditional> 194 </conditional>
163 195
164 <!-- Genome source. --> 196 <!-- Genome source. -->
165 <conditional name="refGenomeSource"> 197 <conditional name="refGenomeSource">
166 <param name="genomeSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options"> 198 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
167 <option value="indexed" selected="True">Use a built-in index</option> 199 <option value="indexed" selected="True">Use a built-in index</option>
168 <option value="history">Index and use a genome fasta and GTF file from history</option> 200 <option value="history">Use reference genome from history and create temporary index</option>
169 </param> 201 </param>
170 <when value="indexed"> 202 <when value="indexed">
171 <param name="index" type="select" label="Select a reference genome"> 203 <conditional name="GTFconditional">
172 <options from_data_table="rnastar_index"> 204 <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
173 <filter type="sort_by" column="2"/> 205 <option value="without-gtf">use genome reference without builtin gene-model</option>
174 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 206 <option value="with-gtf">use genome reference with builtin gene-model</option>
175 </options> 207 </param>
176 </param> 208 <when value="with-gtf">
209 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
210 <options from_data_table="rnastar_index2">
211 <filter type="static_value" column="4" value="1"/>
212 <filter type="sort_by" column="2" />
213 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
214 </options>
215 </param>
216 </when>
217 <when value="without-gtf">
218 <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
219 <options from_data_table="rnastar_index2">
220 <filter type="static_value" column="4" value="0"/>
221 <filter type="sort_by" column="2" />
222 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
223 </options>
224 </param>
225
226 <expand macro="@SJDBOPTIONS@" />
227 </when>
228 </conditional>
177 </when> 229 </when>
178 <when value="history"> 230 <when value="history">
179 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> 231 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
180 <param name="geneModel" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions. Leave blank for none" 232 <expand macro="@SJDBOPTIONS@" />
181 optional="true" help="Optional. If supplied, the index file will retain exon junction information for mapping splices (--sjdbGTFfile)"/>
182 <param name="overhang" type="integer" min="0" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1 (--sjdbOverhang)"/>
183 </when> 233 </when>
184 </conditional> 234 </conditional>
185 235 <param argument="--quantMode" type="boolean" label="Count number of reads per gene" help="column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA , column 4: counts for the 2nd read strand aligned with RNA. This requires either (A) an index that was built with an annotation (GTF or GFF3 file) or (B) having specified an annotation (GTF or GFF3 file above)."/>
236
186 <!-- Output parameter settings. --> 237 <!-- Output parameter settings. -->
187 <conditional name="output_params"> 238 <conditional name="output_params">
188 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?"> 239 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
189 <option value="no" selected="true">No</option>
190 <option value="yes">Yes</option>
191 </param>
192 <when value="yes">
193 <param name="outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below (--outSAMattributes)">
194 <option value="Standard" selected="true">Standard</option>
195 <option value="All">All</option>
196 <option value="None">None</option>
197 </param>
198 <param name="outSAMstrandField" type="select" label="Include strand field flag XS" help="For Cufflinks compatibility with unstranded RNA-seq data, this option is required (--outSAMstrandField)">
199 <option value="None" selected="true">No</option>
200 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
201 </param>
202 <param name="outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended (--outFilterIntronMotifs)">
203 <option value="None" selected="true">No</option>
204 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
205 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
206 </param>
207
208 <!-- Additional output parameter settings. -->
209 <conditional name="output_params2">
210 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
211 <option value="no" selected="true">No</option> 240 <option value="no" selected="true">No</option>
212 <option value="yes">Yes</option> 241 <option value="yes">Yes</option>
213 </param> 242 </param>
214 <when value="yes"> 243 <when value="yes">
215 <param name="unmapped_opt" type="boolean" truevalue="Within" falsevalue="None" checked="false" label="Would you like unmapped reads included in the SAM?" help="(--outSAMunmapped)"/> 244 <param argument="--outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below">
216 <param name="primary_opt" type="boolean" truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" label="Would you like all alignments with the best score labeled primary?" help="(--outSAMprimaryFlag)"/> 245 <option value="Standard" selected="true">Standard</option>
217 <param name="unique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers" help="(--outSAMmapqUnique)"/> 246 <option value="All">All</option>
218 <param name="sjfilter_opt" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?" help="(--outFilterType)"/> 247 <option value="None">None</option>
219 <param name="multiScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments" help="(--outFilterMultimapScoreRange)"/> 248 </param>
220 <param name="multiNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output (--outFilterMultimapNmax)"/> 249 <param argument="--outSAMstrandField" type="select" label="Include strand field flag XS" help="For Cufflinks compatibility with unstranded RNA-seq data, this option is required">
221 <param name="mismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output (--outFilterMismatchNmax)"/> 250 <option value="None" selected="true">No</option>
222 <param name="mismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output (--outFilterMismatchNoverLmax)"/> 251 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
223 <param name="mismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output (--outFilterMismatchNoverReadLmax)"/> 252 </param>
224 <param name="scoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output (--outFilterScoreMin)"/> 253 <param argument="--outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended">
225 <param name="scoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output (--outFilterScoreMinOverLread)"/> 254 <option value="None" selected="true">No</option>
226 <param name="matchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output (--outFilterMatchNmin)"/> 255 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
227 <param name="matchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output (--outFilterMatchNminOverLread)"/> 256 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
228 </when> 257 </param>
229 <when value="no"/> 258
230 </conditional> 259 <!-- Additional output parameter settings. -->
231 260 <conditional name="output_params2">
261 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
262 <option value="no" selected="true">No</option>
263 <option value="yes">Yes</option>
264 </param>
265 <when value="yes">
266 <param argument="--outSAMunmapped" type="boolean" truevalue="Within" falsevalue="None" checked="false" label="Would you like unmapped reads included in the SAM?"/>
267 <param argument="--outSAMprimaryFlag" type="boolean" truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" label="Would you like all alignments with the best score labeled primary?"/>
268 <param argument="--outSAMmapqUnique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers"/>
269 <param argument="--outFilterType" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?"/>
270 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
271 <param argument="--outFilterMultimapNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output"/>
272 <param argument="--outFilterMismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output"/>
273 <param argument="--outFilterMismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
274 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
275 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
276 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
277 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
278 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
279 </when>
280 <when value="no"/>
281 </conditional>
232 </when> 282 </when>
233 <when value="no"/> 283 <when value="no"/>
234 </conditional> 284 </conditional>
235 285
236 <!-- Other parameter settings. --> 286 <!-- Other parameter settings. -->
237 <conditional name="params"> 287 <conditional name="params">
238 <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)"> 288 <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)">
239 <option value="default" selected="true">Use Defaults</option> 289 <option value="default" selected="true">Use Defaults</option>
240 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> 290 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
241 <option value="full">Extended parameter list</option> 291 <option value="full">Extended parameter list</option>
242 </param> 292 </param>
243 <when value="default"/> 293 <when value="default"/>
244 <when value="star_fusion"/> <!-- Set STAR-fusion parameters automatically --> 294 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
245 295
246 <when value="full"> 296 <when value="full">
247 297 <section name="seed" title="Seed parameters" expanded="False">
248 <!-- Seed parameters --> 298 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
249 <conditional name="seed"> 299 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
250 <param name="seed_select" type="select" label="Would you like to set seed parameters?"> 300 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
251 <option value="no" selected="true">No</option> 301 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
252 <option value="yes">Yes</option> 302 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
253 </param> 303 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
254 <when value="yes"> 304 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
255 <param name="searchStart" type="integer" min="1" value="50" label="Search start point through the read" help="(--seedSearchStartLmax)"/> 305 </section>
256 <param name="searchStartNorm" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length" help="(--seedSearchStartLmaxOverLread)"/> 306
257 <param name="searchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length (--seedSearchLmax)"/> 307 <section name="align" title="Alignment parameters" expanded="False">
258 <param name="multimap" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching" help="(--seedMultimapNmax)"/> 308 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
259 <param name="readMax" type="integer" min="1" value="1000" label="Maximum number of seeds per read" help="(--seedPerReadNmax)"/> 309 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
260 <param name="windowMax" type="integer" min="1" value="50" label="Maximum number of seeds per window" help="(--seedPerWindowNmax)"/> 310 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
261 <param name="oneSeed" type="integer" min="1" value="10" label="Maximum number of one seed loci per window" help="(--seedNoneLociPerWindow)"/> 311 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
262 </when> 312 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
263 <when value="no"/> 313 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
264 </conditional> 314 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
265 315 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
266 <!-- Alignment parameters --> 316 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
267 <conditional name="align"> 317 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
268 <param name="align_select" type="select" label="Would you like to set alignment parameters?"> 318 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
269 <option value="no" selected="true">No</option> 319 </section>
270 <option value="yes">Yes</option> 320
271 </param> 321 <conditional name="chim">
272 <when value="yes"> 322 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
273 <param name="intronMin" type="integer" min="0" value="21" label="Minimum intron size" help="(--alignIntronMin)"/> 323 <option value="no" selected="true">No</option>
274 <param name="intronMax" type="integer" min="0" value="0" label="Maximum intron size" help="(--alignIntronMax)"/> 324 <option value="yes">Yes</option>
275 <param name="gapMax" type="integer" min="0" value="0" label="Maximum gap between two mates" help="(--alignMatesGapMax)"/> 325 </param>
276 <param name="sjOverhang" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments" help="(--alignSJoverhangMin)"/> 326 <when value="yes">
277 <param name="sjdbOverhang" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments" help="(--alignSJDBoverhangMin)"/> 327 <param argument="--chimSegmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used. Default of 0 means no chimeric output">
278 <param name="splicedMate" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced" help="(--alignSplicedMateMapLmin)"/> 328 <validator type="in_range" min="1" message="To get chimeric reads this value needs to be larger than 0"/>
279 <param name="splicedMateNorm" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length" help="(--alignSplicedMateMapLminOverLmate)"/> 329 </param>
280 <param name="windows" type="integer" min="1" value="10000" label="Maximum number of windows per read" help="(--alignWindowsPerReadNmax)"/> 330 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/>
281 <param name="transWindow" type="integer" min="1" value="100" label="Maximum number of transcripts per window" help="(--alignTranscriptsPerWindowNmax)"/> 331 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
282 <param name="transRead" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider" help="(--alignTranscriptsPerReadNmax)"/> 332 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
283 <param name="endsType_opt" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?" help="(--alignEndsType)"/> 333 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
284 </when> 334 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
285 <when value="no"/> 335 </when>
286 </conditional> 336 <when value="no"/>
287 337 </conditional>
288 <!-- Chimeric alignment parameters --> 338 </when>
289 <conditional name="chim">
290 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
291 <option value="no" selected="true">No</option>
292 <option value="yes">Yes</option>
293 </param>
294 <when value="yes">
295 <param name="segmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="Default of 0 means no chimeric output (--chimSegmentMin)"/>
296 <param name="scoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments" help="(--chimScoreMin)"/>
297 <param name="scoreDrop" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length" help="(--chimScoreDropMax)"/>
298 <param name="scoreSep" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one" help="(--chimScoreSeparation)"/>
299 <param name="scoreJunction" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction" help="(--chimScoreJunctionNonGTAG)"/>
300 <param name="junctionOverhang" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction" help="(--chimJunctionOverhangMin)"/>
301 </when>
302 <when value="no"/>
303 </conditional>
304
305 </when>
306 </conditional> 339 </conditional>
307
308 </inputs> 340 </inputs>
309 341
310 <outputs> 342 <outputs>
311 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> 343 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
312 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: starchimjunc" from_work_dir="Chimeric.out.junction"> 344 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
313 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter> 345 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
314 <actions> 346 <actions>
315 <conditional name="refGenomeSource.genomeSource"> 347 <conditional name="refGenomeSource.geneSource">
316 <when value="indexed"> 348 <when value="indexed">
317 <action type="metadata" name="dbkey"> 349 <action type="metadata" name="dbkey">
318 <option type="from_data_table" name="rnastar_index" column="1" offset="0"> 350 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
319 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 351 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
320 <filter type="param_value" ref="refGenomeSource.index" column="0"/> 352 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
321 </option> 353 </option>
322 </action> 354 </action>
323 </when> 355 </when>
324 <when value="history"> 356 <when value="history">
325 <action type="metadata" name="dbkey"> 357 <action type="metadata" name="dbkey">
326 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> 358 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
327 </action> 359 </action>
328 </when> 360 </when>
329 </conditional> 361 </conditional>
330 </actions> 362 </actions>
331 </data> 363 </data>
332 364
333 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: starmappedchim.bam" from_work_dir="ChimericSorted.bam"> 365 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
334 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter> 366 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
335 <actions> 367 <actions>
336 <conditional name="refGenomeSource.genomeSource"> 368 <conditional name="refGenomeSource.geneSource">
337 <when value="indexed"> 369 <when value="indexed">
338 <action type="metadata" name="dbkey"> 370 <action type="metadata" name="dbkey">
339 <option type="from_data_table" name="rnastar_index" column="1" offset="0"> 371 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
340 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 372 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
341 <filter type="param_value" ref="refGenomeSource.index" column="0"/> 373 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
342 </option> 374 </option>
343 </action> 375 </action>
344 </when> 376 </when>
345 <when value="history"> 377 <when value="history">
346 <action type="metadata" name="dbkey"> 378 <action type="metadata" name="dbkey">
347 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> 379 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
380 </action>
381 </when>
382 </conditional>
383 </actions>
384 </data>
385
386 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
387 <actions>
388 <conditional name="refGenomeSource.geneSource">
389 <when value="indexed">
390 <action type="metadata" name="dbkey">
391 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
392 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
393 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
394 </option>
395 </action>
396 </when>
397 <when value="history">
398 <action type="metadata" name="dbkey">
399 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
400 </action>
401 </when>
402 </conditional>
403 </actions>
404 </data>
405
406 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
407 <actions>
408 <conditional name="refGenomeSource.geneSource">
409 <when value="indexed">
410 <action type="metadata" name="dbkey">
411 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
412 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
413 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
414 </option>
415 </action>
416 </when>
417 <when value="history">
418 <action type="metadata" name="dbkey">
419 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
348 </action> 420 </action>
349 </when> 421 </when>
350 </conditional> 422 </conditional>
351 </actions> 423 </actions>
352 </data> 424 </data>
353 425
354 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: starsplicejunct.bed" from_work_dir="SJ.out.tab"> 426 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
355 <actions> 427 <filter>quantMode is True</filter>
356 <conditional name="refGenomeSource.genomeSource">
357 <when value="indexed">
358 <action type="metadata" name="dbkey">
359 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
360 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
361 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
362 </option>
363 </action>
364 </when>
365 <when value="history">
366 <action type="metadata" name="dbkey">
367 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
368 </action>
369 </when>
370 </conditional>
371 </actions>
372 </data>
373
374 <data format="bam" name="mapped_reads" label="${tool.name} on ${on_string}: starmapped.bam" from_work_dir="AlignedSorted.bam">
375 <actions>
376 <conditional name="refGenomeSource.genomeSource">
377 <when value="indexed">
378 <action type="metadata" name="dbkey">
379 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
380 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
381 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
382 </option>
383 </action>
384 </when>
385 <when value="history">
386 <action type="metadata" name="dbkey">
387 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
388 </action>
389 </when>
390 </conditional>
391 </actions>
392 </data> 428 </data>
393 </outputs> 429 </outputs>
394 430
395 <tests> 431 <tests>
396 <test> 432 <test>
397 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 433 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
398 <param name="genomeSource" value="history" /> 434 <param name="geneSource" value="history" />
399 <param name="ownFile" value="tophat_test.fa" /> 435 <param name="genomeFastaFiles" value="tophat_test.fa" />
400 <param name="sPaired" value="single" /> 436 <param name="sPaired" value="single" />
401 437
402 <param name="output_select" value="yes" /> 438 <param name="output_select" value="yes" />
403 <param name="outSAMattributes" value="All" /> 439 <param name="outSAMattributes" value="All" />
404 <param name="outSAMstrandField" value="intronMotif" /> 440 <param name="outSAMstrandField" value="intronMotif" />
405 <param name="settingsType" value="default" /> 441 <param name="settingsType" value="default" />
406 442
407 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff = "10"/> 443 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
408 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 444 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
409 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" /> 445 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
446 </test>
447 <test><!-- tests gtf file and GeneCounts mode -->
448 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
449 <param name="geneSource" value="history" />
450 <param name="genomeFastaFiles" value="tophat_test.fa" />
451
452 <param name="sjdbOverhang" value="75"/>
453 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
454 <param name="quantMode" value="True"/>
455
456 <param name="sPaired" value="single" />
457 <param name="output_select" value="yes" />
458 <param name="outSAMattributes" value="All" />
459 <param name="outSAMstrandField" value="intronMotif" />
460 <param name="settingsType" value="default" />
461
462 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
463 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
464 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
465 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
410 </test> 466 </test>
411 <test> 467 <test>
412 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 468 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
413 <param name="genomeSource" value="history" /> 469 <param name="geneSource" value="history" />
414 <param name="ownFile" value="tophat_test.fa" /> 470 <param name="genomeFastaFiles" value="tophat_test.fa" />
415 <param name="sPaired" value="single" /> 471 <param name="sPaired" value="single" />
416 472
417 <param name="output_select" value="yes" /> 473 <param name="output_select" value="yes" />
418 <param name="outSAMattributes" value="All" /> 474 <param name="outSAMattributes" value="All" />
419 <param name="outSAMstrandField" value="intronMotif" /> 475 <param name="outSAMstrandField" value="intronMotif" />
420 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" /> 476 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
421 477
422 <param name="output_select2" value="yes" /> 478 <param name="output_select2" value="yes" />
423 <param name="scoreMinOverLread" value="0.9" /> 479 <param name="outFilterScoreMinOverLread" value="0.9" />
424 <param name="settingsType" value="full" /> 480 <param name="settingsType" value="full" />
425 <param name="seed_select" value="yes" /> 481 <param name="seed_select" value="yes" />
426 <param name="searchStart" value="25" /> 482 <param name="seedSearchStartLmax" value="25" />
427 483
428 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="10"/> 484 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="12"/>
429 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/> 485 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/>
430 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" /> 486 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
431 </test> 487 </test>
432
433 <test> 488 <test>
434 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" /> 489 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
435 <param name="genomeSource" value="history" /> 490 <param name="geneSource" value="history" />
436 <param name="ownFile" value="test3.ref.fa" /> 491 <param name="genomeFastaFiles" value="test3.ref.fa" />
437 <param name="sPaired" value="single" /> 492 <param name="sPaired" value="single" />
438 493
439 <param name="output_select" value="yes" /> 494 <param name="output_select" value="yes" />
440 <param name="outSAMattributes" value="All" /> 495 <param name="outSAMattributes" value="All" />
441 <param name="outSAMstrandField" value="intronMotif" /> 496 <param name="outSAMstrandField" value="intronMotif" />
442 <param name="settingsType" value="star_fusion" /> 497 <param name="settingsType" value="star_fusion" />
443 498
444 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/> 499 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
445 </test> 500 </test>
446 501 <test><!-- tests fastqsanger.gz -->
502 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />
503 <param name="geneSource" value="history" />
504 <param name="genomeFastaFiles" value="test3.ref.fa" />
505 <param name="sPaired" value="single" />
506
507 <param name="output_select" value="yes" />
508 <param name="outSAMattributes" value="All" />
509 <param name="outSAMstrandField" value="intronMotif" />
510 <param name="settingsType" value="star_fusion" />
511
512 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
513 </test>
447 <test> 514 <test>
448 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 515 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
449 <param name="genomeSource" value="history" /> 516 <param name="geneSource" value="history" />
450 <param name="ownFile" value="tophat_test.fa" /> 517 <param name="genomeFastaFiles" value="tophat_test.fa" />
451 <param name="sPaired" value="single" /> 518 <param name="sPaired" value="single" />
452 519
453 <param name="output_select" value="yes" /> 520 <param name="output_select" value="yes" />
454 <param name="outSAMattributes" value="All" /> 521 <param name="outSAMattributes" value="All" />
455 <param name="outSAMstrandField" value="intronMotif" /> 522 <param name="outSAMstrandField" value="intronMotif" />
456 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" /> 523 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
457 524
458 <param name="output_select2" value="yes" /> 525 <param name="output_select2" value="yes" />
459 <param name="settingsType" value="full" /> 526 <param name="settingsType" value="full" />
460 <param name="seed_select" value="yes" /> 527 <param name="chim_select" value="false" />
461 <param name="align_select" value="yes" />
462 <param name="chim_select" value="yes" />
463 528
464 <!-- Uses default settings, should be similar to test1, but tests the parameters --> 529 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
465 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="10"/>
466 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 530 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
467 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /><!-- header is 434 bytes larger --> 531 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
468 </test> 532 </test>
469
470 </tests> 533 </tests>
471 <help> 534 <help>
472 **What it does** 535 **What it does**
473 536
474 This tool runs STAR, an ultrafast universal RNA-seq aligner. 537 STAR is an ultrafast universal RNA-seq aligner.
475 538
476 **Extra SAM attributes** 539 **Extra SAM attributes**
477 540
478 The Standard option includes the following four attributes:: 541 The Standard option includes the following four attributes::
479 542
497 --twopassMode Basic # not an option in STAR 2.4.0 560 --twopassMode Basic # not an option in STAR 2.4.0
498 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0 561 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
499 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0 562 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
500 563
501 **Attributions** 564 **Attributions**
502
503 Note that each component has its own license:
504 - RNA STAR: GPLv3
505 - samtools: MIT/Expat License
506 565
507 rna_star - see the web site at rna_star_ 566 rna_star - see the web site at rna_star_
508 567
509 For details, please see the rna_starMS_ 568 For details, please see the rna_starMS_
510 "STAR: ultrafast universal RNA-seq aligner" 569 "STAR: ultrafast universal RNA-seq aligner"
523 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion 582 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
524 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs 583 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
525 .. _rna_star: https://github.com/alexdobin/STAR 584 .. _rna_star: https://github.com/alexdobin/STAR
526 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full 585 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
527 .. _Galaxy: http://getgalaxy.org 586 .. _Galaxy: http://getgalaxy.org
528 </help> 587 </help>
529 <citations> 588 <expand macro="citations"/>
530 <citation type="doi">10.1093/bioinformatics/bts635</citation>
531 </citations>
532 </tool> 589 </tool>