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comparison featurecounts.xml @ 6:9d60a36b5c6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
author iuc
date Thu, 26 Oct 2017 15:11:19 -0400
parents d417fb66494e
children 3ce1c701b0df
comparison
equal deleted inserted replaced
5:de2c5e5a206c 6:9d60a36b5c6a
1 <tool id="featurecounts" name="featureCounts" version="1.4.6.p5" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.5.3" 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="1.4.6p5">subread</requirement> 4 <requirement type="package" version="1.5.3">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)
10 featureCounts 10 featureCounts
11 #if $gtf_source.ref_source=="history": 11 #if $gtf_source.ref_source=="history":
12 -a "$gtf_source.reference_gene_sets" 12 -a '$gtf_source.reference_gene_sets'
13 #else: 13 #else:
14 -a "$gtf_source.reference_gene_sets_builtin.fields.path" 14 -a '$gtf_source.reference_gene_sets_builtin.fields.path'
15 #end if 15 #end if
16 16
17 -o "output" 17 -o "output"
18 -T \${GALAXY_SLOTS:-2} 18 -T \${GALAXY_SLOTS:-2}
19 19
20 -t "$extended_parameters.gff_feature_type" 20 -t '$extended_parameters.gff_feature_type'
21 -g "$extended_parameters.gff_feature_attribute" 21 -g '$extended_parameters.gff_feature_attribute'
22 $extended_parameters.summarization_level 22 $extended_parameters.summarization_level
23 $extended_parameters.contribute_to_multiple_features 23 $extended_parameters.contribute_to_multiple_features
24 -s $extended_parameters.strand_specificity 24 -s $extended_parameters.strand_specificity
25 $extended_parameters.multimapping_enabled.multimapping_counts 25 $extended_parameters.multimapping_enabled.multimapping_counts
26 26
27 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M" 27 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M"
28 $extended_parameters.multimapping_enabled.fraction 28 $extended_parameters.multimapping_enabled.fraction
29 #end if 29 #end if
30
31 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
32 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
33 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
34 #end if
35
36 $extended_parameters.long_reads
30 37
31 -Q $extended_parameters.mapping_quality 38 -Q $extended_parameters.mapping_quality
32 $extended_parameters.largest_overlap 39 $extended_parameters.largest_overlap
33 --minOverlap $extended_parameters.min_overlap 40 --minOverlap $extended_parameters.min_overlap
34 $extended_parameters.read_reduction 41 $extended_parameters.read_reduction
51 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length 58 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
52 #end if 59 #end if
53 #end if 60 #end if
54 61
55 $pe_parameters.only_both_ends 62 $pe_parameters.only_both_ends
56 -S $pe_parameters.orientation
57 $pe_parameters.exclude_chimerics 63 $pe_parameters.exclude_chimerics
58 64
59 "${alignment}" 65 '${alignment}'
60 66
61 ## Removal of comment and column-header line 67 ## Removal of comment and column-header line
62 && grep -v "^#" "output" | tail -n+2 > body.txt 68 && grep -v "^#" "output" | tail -n+2 > body.txt
63 69
64 ## Set the right columns for the tabular formats 70 ## Set the right columns for the tabular formats
67 73
68 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8 74 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
69 ## Thus the gene length column (last column) has to be added separately 75 ## Thus the gene length column (last column) has to be added separately
70 && cut -f 6 body.txt > gene_lengths.txt 76 && cut -f 6 body.txt > gene_lengths.txt
71 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak 77 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
72 && mv -f expression_matrix.txt.bak "${output_medium}" 78 && mv -f expression_matrix.txt.bak '${output_medium}'
73 #elif $format.value == "tabdel_short" 79 #elif $format.value == "tabdel_short"
74 && cut -f 1,7 body.txt > "${output_short}" 80 && cut -f 1,7 body.txt > '${output_short}'
75 #else 81 #else
76 && cp body.txt "${output_full}" 82 && cp body.txt '${output_full}'
77 #end if 83 #end if
78 84
79 85
80 #if str($include_feature_length_file) == "true" 86 #if str($include_feature_length_file) == "true"
81 && cut -f 1,6 body.txt > "${output_feature_lengths}" 87 && cut -f 1,6 body.txt > '${output_feature_lengths}'
82 #end if 88 #end if
83 89
84 && tail -n+2 "output.summary" > "${output_summary}" 90 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
91 && tail -n+2 'output.jcounts' > '${output_jcounts}'
92 #end if
93
94 && tail -n+2 'output.summary' > '${output_summary}'
85 95
86 ]]></command> 96 ]]></command>
87 <inputs> 97 <inputs>
88 <param name="alignment" 98 <param name="alignment"
89 type="data" 99 type="data"
178 falsevalue="" 188 falsevalue=""
179 argument="-B" 189 argument="-B"
180 label="Only allow fragments with both reads aligned" 190 label="Only allow fragments with both reads aligned"
181 help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." /> 191 help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." />
182 192
183 <param name="orientation"
184 type="select"
185 label="Orientation of the two read from the same pair"
186 argument="-S"
187 help="Default is 'fr'">
188 <option value="fr" selected="true">Forward, Reverse (fr)</option>
189 <option value="ff">Forward, Forward (ff)</option>
190 <option value="rf">Reverse, Forward (rf)</option>
191 </param>
192
193 <param name="exclude_chimerics" 193 <param name="exclude_chimerics"
194 type="boolean" 194 type="boolean"
195 truevalue=" -C" 195 truevalue=" -C"
196 falsevalue="" 196 falsevalue=""
197 argument="-C" 197 argument="-C"
266 type="integer" 266 type="integer"
267 value="12" 267 value="12"
268 argument="-Q" 268 argument="-Q"
269 label="Minimum mapping quality per read" 269 label="Minimum mapping quality per read"
270 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." /> 270 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." />
271
272 <conditional name="exon_exon_junction_read_counting_enabled">
273 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
274 label="Exon-exon junctions"
275 help="If specified, reads supporting each exon-exon junction will be counted" />
276 <when value="-J">
277 <param name="genome" argument="-G" type="data" format="fasta"
278 label="Reference sequence (genome) file"
279 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
280 </when>
281 <when value="" />
282 </conditional>
283
284 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
285 label="Long reads"
286 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." />
271 287
272 <param name="largest_overlap" 288 <param name="largest_overlap"
273 type="boolean" 289 type="boolean"
274 truevalue=" --largestOverlap" 290 truevalue=" --largestOverlap"
275 falsevalue="" 291 falsevalue=""
371 </data> 387 </data>
372 388
373 <data format="tabular" 389 <data format="tabular"
374 name="output_feature_lengths" 390 name="output_feature_lengths"
375 label="${tool.name} on ${on_string}: feature lengths"> 391 label="${tool.name} on ${on_string}: feature lengths">
376 <filter>include_feature_length_file</filter> 392 <filter>include_feature_length_file</filter>
377 <actions> 393 <actions>
378 <action name="column_names" type="metadata" default="Feature,Length" /> 394 <action name="column_names" type="metadata" default="Feature,Length" />
395 </actions>
396 </data>
397
398 <data name="output_jcounts" format="tabular"
399 label="${tool.name} on ${on_string}: junction counts">
400 <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter>
401 <actions>
402 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
379 </actions> 403 </actions>
380 </data> 404 </data>
381 </outputs> 405 </outputs>
382 <tests> 406 <tests>
383 <test> 407 <test>