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comparison featurecounts.xml @ 3:711c80e57384 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
author iuc
date Thu, 10 Nov 2016 03:05:05 -0500
parents 4d0763d3eb93
children 2451333b004b
comparison
equal deleted inserted replaced
2:4d0763d3eb93 3:711c80e57384
6 6
7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
8 <command><![CDATA[ 8 <command><![CDATA[
9 ## Check whether all alignments are from the same type (bam || sam) 9 ## Check whether all alignments are from the same type (bam || sam)
10 featureCounts 10 featureCounts
11 -a "$reference_gene_sets" 11 #if $gtf_source.ref_source=="history":
12 -a "$gtf_source.reference_gene_sets"
13 #else:
14 -a "$gtf_source.reference_gene_sets_builtin.fields.path"
15 #end if
16
12 -o "output" 17 -o "output"
13 -T \${GALAXY_SLOTS:-2} 18 -T \${GALAXY_SLOTS:-2}
14 19
15 -t "$extended_parameters.gff_feature_type" 20 -t "$extended_parameters.gff_feature_type"
16 -g "$extended_parameters.gff_feature_attribute" 21 -g "$extended_parameters.gff_feature_attribute"
23 $extended_parameters.multimapping_enabled.fraction 28 $extended_parameters.multimapping_enabled.fraction
24 #end if 29 #end if
25 30
26 -Q $extended_parameters.mapping_quality 31 -Q $extended_parameters.mapping_quality
27 $extended_parameters.largest_overlap 32 $extended_parameters.largest_overlap
28 --minOverlap $extended_parameters.min_overlap 33 --minOverlap $extended_parameters.min_overlap
29 $extended_parameters.read_reduction 34 $extended_parameters.read_reduction
30 $extended_parameters.primary 35 $extended_parameters.primary
31 $extended_parameters.ignore_dup 36 $extended_parameters.ignore_dup
32 37
33 #if str($extended_parameters.read_extension_5p) != "0" 38 #if str($extended_parameters.read_extension_5p) != "0"
85 multiple="false" 90 multiple="false"
86 format="bam,sam" 91 format="bam,sam"
87 label="Alignment file" 92 label="Alignment file"
88 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" /> 93 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />
89 94
90 <param name="reference_gene_sets" 95 <conditional name="gtf_source">
91 format="gff,gtf,gff3" 96 <param name="ref_source" type="select" label="Gene annotation file">
92 type="data" 97 <option value="cached">locally cached</option>
93 label="Gene annotation file" 98 <option value="history">in your history</option>
94 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" /> 99 </param>
100 <when value="cached">
101 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
102 <options from_data_table="gene_sets">
103 <filter type="sort_by" column="1" />
104 <validator type="no_options" message="No annotations are available." />
105 </options>
106 </param>
107 </when>
108 <when value="history">
109 <param name="reference_gene_sets"
110 format="gff,gtf,gff3"
111 type="data"
112 label="Gene annotation file"
113 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
114 </when>
115 </conditional>
95 116
96 <param name="format" 117 <param name="format"
97 type="select" 118 type="select"
98 label="Output format" 119 label="Output format"
99 help="The output format will be tabular, select the preferred columns here"> 120 help="The output format will be tabular, select the preferred columns here">
206 type="boolean" 227 type="boolean"
207 truevalue=" -O" 228 truevalue=" -O"
208 falsevalue="" 229 falsevalue=""
209 argument="-O" 230 argument="-O"
210 label="Allow read to contribute to multiple features" 231 label="Allow read to contribute to multiple features"
211 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" /> 232 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />
212 233
213 <param name="strand_specificity" 234 <param name="strand_specificity"
214 type="select" 235 type="select"
215 label="Strand specificity of the protocol" 236 label="Strand specificity of the protocol"
216 argument="-s" 237 argument="-s"
279 300
280 <param name="read_reduction" 301 <param name="read_reduction"
281 type="select" 302 type="select"
282 label="Reduce read to single position" 303 label="Reduce read to single position"
283 argument="--read2pos" 304 argument="--read2pos"
284 help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on thesingle base which the read is reduced to."> 305 help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on the single base the the read is reduced to.">
285 <option value="" selected="true">Leave the read as it is</option> 306 <option value="" selected="true">Leave the read as it is</option>
286 <option value="--read2pos 5">Reduce it to the 5' end</option> 307 <option value="--read2pos 5">Reduce it to the 5' end</option>
287 <option value="--read2pos 3">Reduce it to the 3' end</option> 308 <option value="--read2pos 3">Reduce it to the 3' end</option>
288 </param> 309 </param>
289 310
291 type="boolean" 312 type="boolean"
292 truevalue=" --primary" 313 truevalue=" --primary"
293 falsevalue="" 314 falsevalue=""
294 argument="--primary" 315 argument="--primary"
295 label="Only count primary alignments" 316 label="Only count primary alignments"
296 help="If specified, only primary alignments will be counted. Primaryand secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a datasetwill be counted no matter they are from multi-mapping reads ornot ('-M' is ignored)." /> 317 help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." />
297 318
298 <param name="ignore_dup" 319 <param name="ignore_dup"
299 type="boolean" 320 type="boolean"
300 truevalue=" --ignoreDup" 321 truevalue=" --ignoreDup"
301 falsevalue="" 322 falsevalue=""
302 argument="--ignoreDup" 323 argument="--ignoreDup"
303 label="Ignore reads marked as duplicate" 324 label="Ignore reads marked as duplicate"
304 help="If specified, reads that were marked asduplicates will be ignored. Bit Ox400 in FLAG field of SAM/BAMfile is used for identifying duplicate reads. In paired enddata, the entire read pair will be ignored if at least one endis found to be a duplicate read." /> 325 help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />
305 326
306 <param name="count_split_alignments_only" 327 <param name="count_split_alignments_only"
307 type="boolean" 328 type="boolean"
308 truevalue=" --countSplitAlignmentsOnly" 329 truevalue=" --countSplitAlignmentsOnly"
309 falsevalue="" 330 falsevalue=""
310 argument="--countSplitAlignmentsOnly" 331 argument="--countSplitAlignmentsOnly"
311 label="Ignore reads marked as duplicate" 332 label="Ignore unspliced alignments"
312 help="If specified, only split alignments (CIGARstrings containing letter `N') will be counted. All the otheralignments will be ignored. An example of split alignments isthe exon-spanning reads in RNA-seq data." /> 333 help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." />
313 </section> 334 </section>
314 </inputs> 335 </inputs>
315 <outputs> 336 <outputs>
316 <data format="tabular" 337 <data format="tabular"
317 name="output_medium" 338 name="output_medium"
362 <test> 383 <test>
363 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 384 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
364 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 385 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
365 <param name="format" value="tabdel_short" /> 386 <param name="format" value="tabdel_short" />
366 <param name="include_feature_length_file" value="true"/> 387 <param name="include_feature_length_file" value="true"/>
388 <param name="ref_source" value="history" />
367 <output name="output" file="output_1_short.tab"/> 389 <output name="output" file="output_1_short.tab"/>
368 <output name="output_summary" file="output_1_summary.tab"/> 390 <output name="output_summary" file="output_1_summary.tab"/>
369 </test> 391 </test>
370 <test> 392 <test>
371 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 393 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
372 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 394 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
373 <param name="format" value="tabdel_medium" /> 395 <param name="format" value="tabdel_medium" />
374 <param name="include_feature_length_file" value="true"/> 396 <param name="include_feature_length_file" value="true"/>
397 <param name="ref_source" value="history" />
375 <output name="output" file="output_1_medium.tab"/> 398 <output name="output" file="output_1_medium.tab"/>
376 <output name="output_summary" file="output_1_summary.tab"/> 399 <output name="output_summary" file="output_1_summary.tab"/>
377 </test> 400 </test>
378 <test> 401 <test>
379 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 402 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
380 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 403 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
381 <param name="format" value="tabdel_full" /> 404 <param name="format" value="tabdel_full" />
382 <param name="include_feature_length_file" value="true"/> 405 <param name="include_feature_length_file" value="true"/>
406 <param name="ref_source" value="history" />
383 <output name="output" file="output_1_full.tab"/> 407 <output name="output" file="output_1_full.tab"/>
384 <output name="output_summary" file="output_1_summary.tab"/> 408 <output name="output_summary" file="output_1_summary.tab"/>
385 <output name="output_feature_lengths" file="output_feature_lengths.tab"/> 409 <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
386 </test> 410 </test>
387 411
388 <test> 412 <test>
389 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 413 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
390 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 414 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
391 <param name="format" value="tabdel_short" /> 415 <param name="format" value="tabdel_short" />
392 <param name="include_feature_length_file" value="true"/> 416 <param name="include_feature_length_file" value="true"/>
417 <param name="ref_source" value="history" />
393 <output name="output" file="output_2_short.tab"/> 418 <output name="output" file="output_2_short.tab"/>
394 <output name="output_summary" file="output_2_summary.tab"/> 419 <output name="output_summary" file="output_2_summary.tab"/>
395 </test> 420 </test>
396 <test> 421 <test>
397 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 422 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
398 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 423 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
399 <param name="format" value="tabdel_medium" /> 424 <param name="format" value="tabdel_medium" />
400 <param name="include_feature_length_file" value="true"/> 425 <param name="include_feature_length_file" value="true"/>
426 <param name="ref_source" value="history" />
401 <output name="output" file="output_2_medium.tab"/> 427 <output name="output" file="output_2_medium.tab"/>
402 <output name="output_summary" file="output_2_summary.tab"/> 428 <output name="output_summary" file="output_2_summary.tab"/>
403 </test> 429 </test>
404 <test> 430 <test>
405 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 431 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
406 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 432 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
407 <param name="format" value="tabdel_full" /> 433 <param name="format" value="tabdel_full" />
408 <param name="include_feature_length_file" value="true"/> 434 <param name="include_feature_length_file" value="true"/>
435 <param name="ref_source" value="history" />
409 <output name="output" file="output_2_full.tab"/> 436 <output name="output" file="output_2_full.tab"/>
410 <output name="output_summary" file="output_2_summary.tab"/> 437 <output name="output_summary" file="output_2_summary.tab"/>
411 <output name="output_feature_lengths" file="output_feature_lengths.tab"/> 438 <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
412 </test> 439 </test>
413 </tests> 440 </tests>