Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 7:a70a7eebb435 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c
author iuc
date Wed, 16 May 2018 17:31:03 -0400
parents 2055c2667eb3
children d5659efd66aa
comparison
equal deleted inserted replaced
6:2055c2667eb3 7:a70a7eebb435
1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01"> 1 <tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
90 #end if 90 #end if
91 91
92 ## Output parameters 92 ## Output parameters
93 #if str( $output_params.output_select ) == "yes": 93 #if str( $output_params.output_select ) == "yes":
94 --outSAMattributes $output_params.outSAMattributes 94 --outSAMattributes $output_params.outSAMattributes
95 --outSAMstrandField $output_params.outSAMstrandField 95 #if str( $params.settingsType ) != "star_fusion":
96 --outSAMstrandField $output_params.outSAMstrandField
97 #end if
96 --outFilterIntronMotifs $output_params.outFilterIntronMotifs 98 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
99 --outFilterIntronStrands $output_params.outFilterIntronStrands
97 #if str( $output_params.output_params2.output_select2 ) == "yes": 100 #if str( $output_params.output_params2.output_select2 ) == "yes":
98 --outSAMunmapped $output_params.output_params2.outSAMunmapped 101 --outSAMunmapped $output_params.output_params2.outSAMunmapped
99 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag 102 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
100 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique" 103 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique"
101 --outFilterType $output_params.output_params2.outFilterType 104 --outFilterType $output_params.output_params2.outFilterType
106 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax" 109 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax"
107 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin" 110 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin"
108 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread" 111 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
109 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin" 112 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
110 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread" 113 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
114 --outSAMmultNmax "$output_params.output_params2.outSAMmultNmax"
115 --outSAMtlen "$output_params.output_params2.outSAMtlen"
116 --outBAMsortingBinsN "$output_params.output_params2.outBAMsortingBinsN"
111 #end if 117 #end if
112 #end if 118 #end if
113 119
114 ## Other parameters 120 ## Other parameters
115 #if str( $params.settingsType ) == "star_fusion": 121 #if str( $params.settingsType ) == "star_fusion":
120 --alignSJDBoverhangMin 10 126 --alignSJDBoverhangMin 10
121 --alignMatesGapMax 200000 127 --alignMatesGapMax 200000
122 --alignIntronMax 200000 128 --alignIntronMax 200000
123 --twopassMode Basic 129 --twopassMode Basic
124 --twopass1readsN -1 130 --twopass1readsN -1
125 131 --chimSegmentReadGapMax 3
126 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0 132 --alignSJstitchMismatchNmax 5 -1 5 5
127 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0 133 --outSAMstrandField intronMotif
128 134
129 #elif str( $params.settingsType ) == "full": 135 #elif str( $params.settingsType ) == "full":
130 ## Extended parameter options 136 ## Extended parameter options
131 137
132 ## Seed parameter options 138 ## Seed parameter options
157 --twopass1readsN "$params.twopass.twopass1readsN" 163 --twopass1readsN "$params.twopass.twopass1readsN"
158 #end if 164 #end if
159 165
160 ## Chimeric alignment parameter options 166 ## Chimeric alignment parameter options
161 #if str( $params.chim.chim_select ) == "yes": 167 #if str( $params.chim.chim_select ) == "yes":
168 --chimOutType Junctions SeparateSAMold
162 --chimSegmentMin "$params.chim.chimSegmentMin" 169 --chimSegmentMin "$params.chim.chimSegmentMin"
163 --chimScoreMin "$params.chim.chimScoreMin" 170 --chimScoreMin "$params.chim.chimScoreMin"
164 --chimScoreDropMax "$params.chim.chimScoreDropMax" 171 --chimScoreDropMax "$params.chim.chimScoreDropMax"
165 --chimScoreSeparation "$params.chim.chimScoreSeparation" 172 --chimScoreSeparation "$params.chim.chimScoreSeparation"
166 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG" 173 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
167 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin" 174 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
175 --chimMainSegmentMultNmax "$params.chim.chimMainSegmentMultNmax"
176 --chimMultimapNmax "$params.chim.chimMultimapNmax"
177 --chimMultimapScoreRange "$params.chim.chimMultimapScoreRange"
168 #end if 178 #end if
169 179
170 ## Limits 180 ## Limits
171 --limitBAMsortRAM "$params.limits.limitBAMsortRAM" 181 --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
172 --limitOutSJoneRead "$params.limits.limitOutSJoneRead" 182 --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
174 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj" 184 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"
175 185
176 #end if 186 #end if
177 187
178 ## Convert chimeric reads. 188 ## Convert chimeric reads.
179 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ): 189 #if str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0:
180 && 190 &&
181 samtools view 191 samtools sort -@ \${GALAXY_SLOTS:-4} -o ChimericSorted.bam -O BAM Chimeric.out.sam
182 -@ \${GALAXY_SLOTS:-4}
183 -Shb Chimeric.out.sam |
184
185 samtools sort
186 -@ \${GALAXY_SLOTS:-4} - ChimericSorted
187 #end if 192 #end if
188 ]]></command> 193 ]]></command>
189 194
190 <inputs> 195 <inputs>
191 <!-- FASTQ input(s) and options specifically for paired-end data. --> 196 <!-- FASTQ input(s) and options specifically for paired-end data. -->
266 </param> 271 </param>
267 <param argument="--outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended"> 272 <param argument="--outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended">
268 <option value="None" selected="true">No</option> 273 <option value="None" selected="true">No</option>
269 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option> 274 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
270 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option> 275 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
276 </param>
277 <param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands">
278 <option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option>
279 <option value="None">No filtering</option>
271 </param> 280 </param>
272 281
273 <!-- Additional output parameter settings. --> 282 <!-- Additional output parameter settings. -->
274 <conditional name="output_params2"> 283 <conditional name="output_params2">
275 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?"> 284 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
288 <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"/> 297 <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"/>
289 <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"/> 298 <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"/>
290 <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"/> 299 <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"/>
291 <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"/> 300 <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"/>
292 <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"/> 301 <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"/>
302 <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" />
303 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
304 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
305 <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
306 </param>
307 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50."/>
293 </when> 308 </when>
294 <when value="no"/> 309 <when value="no"/>
295 </conditional> 310 </conditional>
296 </when> 311 </when>
297 <when value="no"/> 312 <when value="no"/>
356 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/> 371 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/>
357 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/> 372 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
358 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/> 373 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
359 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/> 374 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
360 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/> 375 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
376 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10" label="Maximum number of multi-alignments for the main chimeric segment." help="A value of 1 prohibits multimapping main segments"/>
377 <param argument="--chimMultimapNmax" type="integer" min="0" value="0" label="Maximum number of chimeric multi-alignments" help="A value of 0 (the default) only considers unique alignments" />
378 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" label="Score range for multi-mapping chimeras" help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
361 </when> 379 </when>
362 <when value="no"/> 380 <when value="no"/>
363 </conditional> 381 </conditional>
364 </when> 382 </when>
365 </conditional> 383 </conditional>
387 </conditional> 405 </conditional>
388 </actions> 406 </actions>
389 </data> 407 </data>
390 408
391 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam"> 409 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
392 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter> 410 <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter>
393 <actions> 411 <actions>
394 <conditional name="refGenomeSource.geneSource"> 412 <conditional name="refGenomeSource.geneSource">
395 <when value="indexed"> 413 <when value="indexed">
396 <action type="metadata" name="dbkey"> 414 <action type="metadata" name="dbkey">
397 <option type="from_data_table" name="rnastar_index" column="1" offset="0"> 415 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
579 jI: Start and end of introns for all junctions 597 jI: Start and end of introns for all junctions
580 598
581 **STAR-Fusion** 599 **STAR-Fusion**
582 600
583 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running 601 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
584 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions:: 602 STAR prior to STAR-Fusion can be pre-selected.
585
586 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
587 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
588 603
589 **Attributions** 604 **Attributions**
590 605
591 rna_star - see the web site at rna_star_ 606 rna_star - see the web site at rna_star_
592 607