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comparison featurecounts.xml @ 8:bff059ad4d13 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
author iuc
date Wed, 15 Nov 2017 15:53:09 -0500
parents 889d2cd8a809
children 81e9f94f257c
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7:889d2cd8a809 8:bff059ad4d13
1 <tool id="featurecounts" name="featureCounts" version="1.5.3" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.0" profile="16.04">
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5.3">subread</requirement> 4 <requirement type="package" version="1.6.0">subread</requirement>
5 </requirements> 5 </requirements>
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)
35 #end if 35 #end if
36 #end if 36 #end if
37 37
38 $extended_parameters.long_reads 38 $extended_parameters.long_reads
39 39
40 $extended_parameters.by_read_group
41
40 -Q $extended_parameters.mapping_quality 42 -Q $extended_parameters.mapping_quality
41 $extended_parameters.largest_overlap 43 $extended_parameters.largest_overlap
42 --minOverlap $extended_parameters.min_overlap 44 --minOverlap $extended_parameters.min_overlap
45 --fracOverlap $extended_parameters.frac_overlap
46 --fracOverlapFeature $extended_parameters.frac_overlap_feature
43 $extended_parameters.read_reduction 47 $extended_parameters.read_reduction
44 $extended_parameters.primary 48 $extended_parameters.primary
45 $extended_parameters.ignore_dup 49 $extended_parameters.ignore_dup
46 50
47 #if str($extended_parameters.read_extension_5p) != "0" 51 #if str($extended_parameters.read_extension_5p) != "0"
81 #elif $format.value == "tabdel_short" 85 #elif $format.value == "tabdel_short"
82 && cut -f 1,7 body.txt > '${output_short}' 86 && cut -f 1,7 body.txt > '${output_short}'
83 #else 87 #else
84 && cp body.txt '${output_full}' 88 && cp body.txt '${output_full}'
85 #end if 89 #end if
86 90
87 91
88 #if str($include_feature_length_file) == "true" 92 #if str($include_feature_length_file) == "true"
89 && cut -f 1,6 body.txt > '${output_feature_lengths}' 93 && cut -f 1,6 body.txt > '${output_feature_lengths}'
90 #end if 94 #end if
91 95
101 type="data" 105 type="data"
102 multiple="false" 106 multiple="false"
103 format="bam,sam" 107 format="bam,sam"
104 label="Alignment file" 108 label="Alignment file"
105 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" /> 109 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" />
106 110
107 <conditional name="gtf_source"> 111 <conditional name="gtf_source">
108 <param name="ref_source" type="select" label="Gene annotation file"> 112 <param name="ref_source" type="select" label="Gene annotation file">
109 <option value="cached">locally cached</option> 113 <option value="cached">locally cached</option>
110 <option value="history">in your history</option> 114 <option value="history">in your history</option>
111 </param> 115 </param>
123 type="data" 127 type="data"
124 label="Gene annotation file" 128 label="Gene annotation file"
125 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" /> 129 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" />
126 </when> 130 </when>
127 </conditional> 131 </conditional>
128 132
129 <param name="format" 133 <param name="format"
130 type="select" 134 type="select"
131 label="Output format" 135 label="Output format"
132 help="The output format will be tabular, select the preferred columns here"> 136 help="The output format will be tabular, select the preferred columns here">
133 <option value="tabdel_short" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option> 137 <option value="tabdel_short" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
134 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option> 138 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
135 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option> 139 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
136 </param> 140 </param>
137 141
138 <param name="include_feature_length_file" 142 <param name="include_feature_length_file"
139 type="boolean" 143 type="boolean"
140 truevalue="true" 144 truevalue="true"
141 falsevalue="false" 145 falsevalue="false"
142 checked="false" 146 checked="false"
181 <when value="" /> 185 <when value="" />
182 </conditional> 186 </conditional>
183 </when> 187 </when>
184 <when value="" /> 188 <when value="" />
185 </conditional> 189 </conditional>
186 190
187 <param name="only_both_ends" 191 <param name="only_both_ends"
188 type="boolean" 192 type="boolean"
189 truevalue=" -B" 193 truevalue=" -B"
190 falsevalue="" 194 falsevalue=""
191 argument="-B" 195 argument="-B"
199 argument="-C" 203 argument="-C"
200 checked="true" 204 checked="true"
201 label="Exclude chimeric fragments" 205 label="Exclude chimeric fragments"
202 help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." /> 206 help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." />
203 </section> 207 </section>
204 208
205 <section name="extended_parameters" title="Advanced options"> 209 <section name="extended_parameters" title="Advanced options">
206 <param name="gff_feature_type" 210 <param name="gff_feature_type"
207 type="text" 211 type="text"
208 value="exon" 212 value="exon"
209 argument="-t" 213 argument="-t"
285 289
286 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" 290 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
287 label="Long reads" 291 label="Long reads"
288 help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." /> 292 help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." />
289 293
294 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
295 label="Count reads by read group"
296 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." />
297
298
290 <param name="largest_overlap" 299 <param name="largest_overlap"
291 type="boolean" 300 type="boolean"
292 truevalue=" --largestOverlap" 301 truevalue=" --largestOverlap"
293 falsevalue="" 302 falsevalue=""
294 argument="--largestOverlap" 303 argument="--largestOverlap"
297 306
298 <param name="min_overlap" 307 <param name="min_overlap"
299 type="integer" 308 type="integer"
300 value="1" 309 value="1"
301 argument="--minOverlap" 310 argument="--minOverlap"
302 label="Minimum overlap" 311 label="Minimum bases of overlap"
303 help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." /> 312 help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." />
313
314 <param name="frac_overlap"
315 type="integer"
316 value="0"
317 min="0"
318 max="1"
319 argument="--fracOverlap"
320 label="Minimum fraction (of read) overlapping a feature"
321 help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." />
322
323 <param name="frac_overlap_feature"
324 type="integer"
325 value="0"
326 min="0"
327 max="1"
328 argument="--fracOverlapFeature"
329 label="Minimum fraction (of feature) overlapping a read"
330 help="Specify the minimum required fraction of bases included in a feature overlapping bases between a read (or a read-pair). Value should be within range [0,1]. 0 by default." />
304 331
305 <param name="read_extension_5p" 332 <param name="read_extension_5p"
306 type="integer" 333 type="integer"
307 value="0" 334 value="0"
308 argument="--readExtension5" 335 argument="--readExtension5"
323 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."> 350 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.">
324 <option value="" selected="true">Leave the read as it is</option> 351 <option value="" selected="true">Leave the read as it is</option>
325 <option value="--read2pos 5">Reduce it to the 5' end</option> 352 <option value="--read2pos 5">Reduce it to the 5' end</option>
326 <option value="--read2pos 3">Reduce it to the 3' end</option> 353 <option value="--read2pos 3">Reduce it to the 3' end</option>
327 </param> 354 </param>
328 355
329 <param name="primary" 356 <param name="primary"
330 type="boolean" 357 type="boolean"
331 truevalue=" --primary" 358 truevalue=" --primary"
332 falsevalue="" 359 falsevalue=""
333 argument="--primary" 360 argument="--primary"
334 label="Only count primary alignments" 361 label="Only count primary alignments"
335 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)." /> 362 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)." />
336 363
337 <param name="ignore_dup" 364 <param name="ignore_dup"
338 type="boolean" 365 type="boolean"
339 truevalue=" --ignoreDup" 366 truevalue=" --ignoreDup"
340 falsevalue="" 367 falsevalue=""
341 argument="--ignoreDup" 368 argument="--ignoreDup"
342 label="Ignore reads marked as duplicate" 369 label="Ignore reads marked as duplicate"
343 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." /> 370 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." />
344 371
345 <param name="count_split_alignments_only" 372 <param name="count_split_alignments_only"
346 type="boolean" 373 type="boolean"
347 truevalue=" --countSplitAlignmentsOnly" 374 truevalue=" --countSplitAlignmentsOnly"
348 falsevalue="" 375 falsevalue=""
349 argument="--countSplitAlignmentsOnly" 376 argument="--countSplitAlignmentsOnly"
450 </output> 477 </output>
451 <output name="output_feature_lengths" file="output_feature_lengths.tab"> 478 <output name="output_feature_lengths" file="output_feature_lengths.tab">
452 <metadata name="column_names" value="Feature,Length"/> 479 <metadata name="column_names" value="Feature,Length"/>
453 </output> 480 </output>
454 </test> 481 </test>
455 482
456 </tests> 483 </tests>
457 484
458 <help><![CDATA[ 485 <help><![CDATA[
459 featureCounts 486 featureCounts
460 ############# 487 #############
461 488
462 Overview 489 Overview