featurecounts: featurecounts.xml annotate

annotate featurecounts.xml @ 24:a37612abf7f9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"

author	iuc
date	Fri, 06 Sep 2019 11:08:21 -0400
parents	9301937c9037
children	90d16db017d7

rev	line source
24 a37612abf7f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 23 diff changeset	1 <tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04">
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	3 <requirements>
23 9301937c9037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d iuc parents: 22 diff changeset	4 <requirement type="package" version="1.6.4">subread</requirement>
21 c946f28be33b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a956e32b176d645db54db3c86586cc0bfa2fbd3c iuc parents: 20 diff changeset	5 <requirement type="package" version="1.9">samtools</requirement>
23 9301937c9037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d iuc parents: 22 diff changeset	6 <requirement type="package" version="8.31">coreutils</requirement>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	7 </requirements>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	8
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	9 <version_command>featureCounts -v 2>&1 \| grep .</version_command>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	10 <command detect_errors="exit_code"><![CDATA[
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	11
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	12 ## Export fc path for its built-in annotation
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	13
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	14 export FC_PATH=\$(command -v featureCounts \| sed 's@/bin/featureCounts$@@') &&
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	15
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	16 ## Check whether all alignments are from the same type (bam \|\| sam)
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	17 featureCounts
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	18
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	19 #if $anno.anno_select=="history":
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	20 -a '$anno.reference_gene_sets'
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	21 -F "GTF"
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	22 #elif $anno.anno_select=="cached":
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	23 -a '$anno.reference_gene_sets_builtin.fields.path'
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	24 -F "GTF"
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	25 #elif $anno.anno_select=="builtin":
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	26 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	27 -F "SAF"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	28 #end if
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	29
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	30 -o "output"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	31 -T \${GALAXY_SLOTS:-2}
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	32
14 85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	33 -s $strand_specificity
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	34 -t '$extended_parameters.gff_feature_type'
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	35 -g '$extended_parameters.gff_feature_attribute'
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	36 $extended_parameters.summarization_level
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	37 $extended_parameters.contribute_to_multiple_features
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	38 $extended_parameters.multimapping_enabled.multimapping_counts
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	39
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	40 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	41 $extended_parameters.multimapping_enabled.fraction
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	42 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	43
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	44 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	45 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	46 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
7 3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	47 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	48 #end if
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	49 #end if
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	50
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	51 $extended_parameters.long_reads
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	52
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	53 $extended_parameters.by_read_group
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	54
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	55 -Q $extended_parameters.mapping_quality
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	56 $extended_parameters.largest_overlap
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	57 --minOverlap $extended_parameters.min_overlap
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	58 --fracOverlap $extended_parameters.frac_overlap
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	59 --fracOverlapFeature $extended_parameters.frac_overlap_feature
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	60 $extended_parameters.read_reduction
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	61 $extended_parameters.primary
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	62 $extended_parameters.ignore_dup
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	63 #if $extended_parameters.R:
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	64 $extended_parameters.R
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	65 #end if
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	66 #if str($extended_parameters.read_extension_5p) != "0":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	67 --readExtension5 $extended_parameters.read_extension_5p
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	68 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	69
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	70 #if str($extended_parameters.read_extension_3p) != "0":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	71 --readExtension3 $extended_parameters.read_extension_3p
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	72 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	73
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	74 $pe_parameters.fragment_counting_enabled.fragment_counting
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	75 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	76 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	77 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	78 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	79 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	80 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	81 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	82
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	83 $pe_parameters.only_both_ends
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	84 $pe_parameters.exclude_chimerics
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	85
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	86 '${alignment}'
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	87
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	88 ## Remove comment and add sample name to header
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	89 && grep -v "^#" "output"
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	90 \| sed -e 's\|${alignment}\|${alignment.element_identifier}\|g'
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	91 > body.txt
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	92 ## Set the right columns for the tabular formats
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	93 #if $format.value == "tabdel_medium":
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	94 && cut -f 1,7 body.txt > expression_matrix.txt
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	95
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	96 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	97 ## Thus the gene length column (last column) has to be added separately
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	98 && cut -f 6 body.txt > gene_lengths.txt
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	99 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	100 && mv -f expression_matrix.txt.bak '${output_medium}'
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	101 #elif $format.value == "tabdel_short":
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	102 && cut -f 1,7 body.txt > '${output_short}'
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	103 #else:
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	104 && cp body.txt '${output_full}'
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	105 #end if
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	106
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	107 #if str($include_feature_length_file) == "true":
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	108 && cut -f 1,6 body.txt > '${output_feature_lengths}'
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	109 #end if
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	110
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	111 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	112 && sed -e 's\|${alignment}\|${alignment.element_identifier}\|g' 'output.jcounts' > '${output_jcounts}'
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	113 #end if
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	114
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	115 #if $extended_parameters.R:
24 a37612abf7f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 23 diff changeset	116 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	117 #end if
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	118 && sed -e 's\|${alignment}\|${alignment.element_identifier}\|g' 'output.summary' > '${output_summary}'
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	119 ]]></command>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	120 <inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	121 <param name="alignment"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	122 type="data"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	123 multiple="false"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	124 format="bam,sam"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	125 label="Alignment file"
12 b714f4620411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 5c013729eeb48f723f7d436c4ded998c8d9291eb iuc parents: 11 diff changeset	126 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. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	127 </param>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	128
14 85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	129 <param name="strand_specificity"
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	130 type="select"
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	131 label="Specify strand information"
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	132 argument="-s"
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	133 help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)">
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	134 <option value="0" selected="true">Unstranded</option>
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	135 <option value="1">Stranded (Forward)</option>
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	136 <option value="2">Stranded (Reverse)</option>
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	137 </param>
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	138
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	139 <conditional name="anno">
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	140 <param name="anno_select" type="select" label="Gene annotation file">
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	141 <option value="builtin">featureCounts built-in</option>
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	142 <option value="cached" selected="True">locally cached</option>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	143 <option value="history">in your history</option>
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	144 </param>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	145 <when value="builtin">
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	147 <options from_data_table="featurecounts_anno">
24 a37612abf7f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 23 diff changeset	148 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	149 </options>
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	150 </param>
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	151 </when>
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	152 <when value="cached">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	153 <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">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	154 <options from_data_table="gene_sets">
24 a37612abf7f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 23 diff changeset	155 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
a37612abf7f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 23 diff changeset	156 <filter type="sort_by" column="2" />
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	157 </options>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	158 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	159 </param>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	160 </when>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	161 <when value="history">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	162 <param name="reference_gene_sets"
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	163 format="gff,gtf,gff3"
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	164 type="data"
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	165 label="Gene annotation file"
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	166 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">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	167 </param>
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	168 </when>
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	169 </conditional>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	170
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	171 <param name="format"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	172 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	173 label="Output format"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	174 help="The output format will be tabular, select the preferred columns here">
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	175 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	176 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	177 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	178 </param>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	179
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	180 <param name="include_feature_length_file"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	181 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	182 truevalue="true"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	183 falsevalue="false"
2 a80f96e55958 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 9a92d439f147a5cf2370e0686854911107de1144 iuc parents: 1 diff changeset	184 checked="false"
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	185 label="Create gene-length file"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	186 help="Creates a tabular file that contains the effective (nucleotides used for counting reads) length of the feature; might be useful for estimating FPKM/RPKM" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	187
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	188
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	189 <section name="pe_parameters" title="Options for paired-end reads">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	190 <conditional name="fragment_counting_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	191
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	192 <param name="fragment_counting"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	193 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	194 argument="-p"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	195 checked="true"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	196 label="Count fragments instead of reads"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	197 help="If specified, fragments (or templates) will be counted instead of reads.">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	198 <option value="" selected="true">Disabled; all reads/mates will be counted individually</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	199 <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	200 </param>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	201
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	202 <when value=" -p">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	203 <conditional name="check_distance_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	204 <param name="check_distance"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	205 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	206 truevalue=" -P"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	207 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	208 argument="-P"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	209 label="Check paired-end distance"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	210 help="If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	211 <when value=" -P">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	212 <param name="minimum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	213 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	214 value="50"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	215 argument="-d"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	216 label="Minimum fragment/template length." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	217 <param name="maximum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	218 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	219 value="600"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	220 argument="-D"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	221 label="Maximum fragment/template length." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	222 </when>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	223 <when value="" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	224 </conditional>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	225 </when>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	226 <when value="" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	227 </conditional>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	228
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	229 <param name="only_both_ends"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	230 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	231 truevalue=" -B"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	232 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	233 argument="-B"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	234 label="Only allow fragments with both reads aligned"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	235 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." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	236
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	237 <param name="exclude_chimerics"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	238 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	239 truevalue=" -C"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	240 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	241 argument="-C"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	242 checked="true"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	243 label="Exclude chimeric fragments"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	244 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." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	245 </section>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	246
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	247 <section name="extended_parameters" title="Advanced options">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	248 <param name="gff_feature_type"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	249 type="text"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	250 value="exon"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	251 argument="-t"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	252 label="GFF feature type filter"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	253 help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	254
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	255 <param name="gff_feature_attribute"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	256 type="text"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	257 value="gene_id"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	258 argument="-g"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	259 label="GFF gene identifier"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	260 help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	261
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	262 <param name="summarization_level"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	263 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	264 truevalue=" -f"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	265 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	266 argument="-f"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	267 label="On feature level"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	268 help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	269
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	270 <param name="contribute_to_multiple_features"
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	271 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	272 truevalue=" -O"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	273 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	274 argument="-O"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	275 label="Allow read to contribute to multiple features"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	276 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)" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	277
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	278 <conditional name="multimapping_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	279 <param name="multimapping_counts"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	280 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	281 argument="-M"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	282 label="Count multi-mapping reads/fragments"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	283 help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads.">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	284 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	285 <option value=" -M">Enabled; multi-mapping reads are included</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	286 </param>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	287 <when value=" -M">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	288 <param name="fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	289 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	290 truevalue="--fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	291 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	292 argument="--fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	293 label="Assign fractions to multimapping reads"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	294 help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read. This option must be used together with the '-M' option." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	295 </when>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	296 <when value="" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	297 </conditional>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	298
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	299 <param name="mapping_quality"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	300 type="integer"
23 9301937c9037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d iuc parents: 22 diff changeset	301 value="0"
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	302 argument="-Q"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	303 label="Minimum mapping quality per read"
23 9301937c9037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d iuc parents: 22 diff changeset	304 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. 0 by default." />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	305
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	306 <conditional name="exon_exon_junction_read_counting_enabled">
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	307 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	308 label="Exon-exon junctions"
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	309 help="If specified, reads supporting each exon-exon junction will be counted" />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	310 <when value="-J">
7 3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	311 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	312 label="Reference sequence file"
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	313 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	314 </when>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	315 <when value="" />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	316 </conditional>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	317
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	318 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	319 label="Long reads"
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	320 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." />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	321
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	322 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	323 label="Count reads by read group"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	324 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." />
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	325
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	326
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	327 <param name="largest_overlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	328 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	329 truevalue=" --largestOverlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	330 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	331 argument="--largestOverlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	332 label="Largest overlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	333 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	334
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	335 <param name="min_overlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	336 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	337 value="1"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	338 argument="--minOverlap"
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	339 label="Minimum bases of overlap"
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	340 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." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	341
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	342 <param name="frac_overlap"
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	343 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	344 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	345 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	346 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	347 argument="--fracOverlap"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	348 label="Minimum fraction (of read) overlapping a feature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	349 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." />
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	350
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	351 <param name="frac_overlap_feature"
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	352 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	353 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	354 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	355 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	356 argument="--fracOverlapFeature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	357 label="Minimum fraction (of feature) overlapping a read"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	358 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." />
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	359
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	360 <param name="read_extension_5p"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	361 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	362 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	363 argument="--readExtension5"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	364 label="Read 5' extension"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	365 help="Reads are extended upstream by ... bases from their 5' end" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	366
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	367 <param name="read_extension_3p"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	368 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	369 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	370 argument="--readExtension3"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	371 label="Read 3' extension"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	372 help="Reads are extended upstream by ... bases from their 3' end" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	373
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	374 <param name="read_reduction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	375 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	376 label="Reduce read to single position"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	377 argument="--read2pos"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	378 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.">
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	379 <option value="" selected="true">Leave the read as it is</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	380 <option value="--read2pos 5">Reduce it to the 5' end</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	381 <option value="--read2pos 3">Reduce it to the 3' end</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	382 </param>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	383
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	384 <param name="primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	385 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	386 truevalue=" --primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	387 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	388 argument="--primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	389 label="Only count primary alignments"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	390 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)." />
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	391
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	392 <param name="ignore_dup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	393 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	394 truevalue=" --ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	395 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	396 argument="--ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	397 label="Ignore reads marked as duplicate"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	398 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." />
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	399
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	400 <param type="boolean"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	401 truevalue="-R BAM"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	402 falsevalue=""
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	403 argument="-R"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	404 label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	405 help="" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	406
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	407 <param name="count_split_alignments_only"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	408 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	409 truevalue=" --countSplitAlignmentsOnly"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	410 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	411 argument="--countSplitAlignmentsOnly"
3 dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	412 label="Ignore unspliced alignments"
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	413 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." />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	414 </section>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	415 </inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	416 <outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	417 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	418 name="output_medium"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	419 label="${tool.name} on ${on_string}: Counts (with length)">
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	420 <filter>format == "tabdel_medium"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	421 <actions>
9 e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138 iuc parents: 8 diff changeset	422 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	423 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	424 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	425
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	426 <data format="bam"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	427 name="output_bam"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	428 label="${tool.name} on ${on_string}: Alignment file">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	429 <filter>extended_parameters['R']</filter>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	430 </data>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	431
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	432 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	433 name="output_short"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	434 label="${tool.name} on ${on_string}: Counts">
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	435 <filter>format == "tabdel_short"</filter>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	436 <actions>
9 e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138 iuc parents: 8 diff changeset	437 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	438 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	439 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	440
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	441 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	442 name="output_full"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	443 label="${tool.name} on ${on_string}: Counts (with location)">
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	444 <filter>format == "tabdel_full"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	445 <actions>
9 e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138 iuc parents: 8 diff changeset	446 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	447 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	448 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	449
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	450 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	451 name="output_summary"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	452 label="${tool.name} on ${on_string}: Summary">
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	453 <actions>
9 e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138 iuc parents: 8 diff changeset	454 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	455 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	456 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	457
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	458 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	459 name="output_feature_lengths"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	460 label="${tool.name} on ${on_string}: Feature lengths">
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	461 <filter>include_feature_length_file</filter>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	462 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	463 <action name="column_names" type="metadata" default="Feature,Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	464 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	465 </data>
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	466
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	467 <data name="output_jcounts" format="tabular"
20 1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	468 label="${tool.name} on ${on_string}: Junction counts">
7 3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	469 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	470 <actions>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	471 <action name="column_names" type="metadata"
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	472 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
6 9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	473 </actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	474 </data>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	475 </outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	476 <tests>
7 3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	477 <test expect_num_outputs="3">
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	478 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	479 <param name="anno_select" value="history"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	480 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	481 <param name="format" value="tabdel_medium" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	482 <param name="include_feature_length_file" value="true"/>
4 d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	483 <output name="output_medium" file="output_1_medium.tab">
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	484 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	485 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	486 <output name="output_summary" file="output_1_summary.tab">
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	487 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	488 </output>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	489 </test>
7 3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	490 <test expect_num_outputs="3">
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	491 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	492 <param name="anno_select" value="history"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	493 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	494 <param name="format" value="tabdel_full" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	495 <param name="include_feature_length_file" value="true"/>
4 d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	496 <output name="output_full" file="output_1_full.tab">
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	497 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	498 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	499 <output name="output_summary" file="output_1_summary.tab">
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	500 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	501 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	502 <output name="output_feature_lengths" file="output_feature_lengths.tab">
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	503 <metadata name="column_names" value="Feature,Length"/>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	504 </output>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	505 </test>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	506 <test expect_num_outputs="4">
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	507 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	508 <param name="anno_select" value="history"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	509 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	510 <param name="format" value="tabdel_short" />
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	511 <param name="include_feature_length_file" value="true"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	512 <param name="count_exon_exon_junction_reads" value="-J"/>
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	513 <output name="output_short" file="output_1_short.tab">
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	514 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	515 </output>
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	516 <output name="output_summary" file="output_1_summary.tab">
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	517 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	518 </output>
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	519 <output name="output_jcounts" file="output_1_jcounts.tab">
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	520 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	521 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	522 </test>
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	523 <!-- Ensure featureCounts built-in annotation works -->
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	524 <test expect_num_outputs="3">
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	525 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	526 <param name="anno_select" value="builtin"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	527 <param name="format" value="tabdel_short" />
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	528 <section name="extended_parameters">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	529 <param name="R" value="true" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	530 </section>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	531 <output name="output_short" file="output_builtin_hg19.tab">
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	532 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	533 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	534 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
17 8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	535 <output name="output_bam" file="output.bam" ftype="bam"/>
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	536 </test>
11 e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	537 <!-- Ensure cached GTFs work -->
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	538 <test expect_num_outputs="3">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	539 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	540 <param name="anno_select" value="cached"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	541 <param name="format" value="tabdel_medium" />
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	542 <param name="include_feature_length_file" value="true"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	543 <output name="output_medium" file="output_1_medium.tab">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	544 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	545 </output>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	546 <output name="output_summary" file="output_1_summary.tab">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	547 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	548 </output>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	549 </test>
18 d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	550 <!-- Ensure BAM output works -->
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	551 <test>
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	552 <param name="alignment" value="subset.sorted.bam" ftype="bam" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	553 <param name="anno_select" value="history" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	554 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	555 <section name="extended_parameters" >
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	556 <param name="R" value="true" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	557 </section>
21 c946f28be33b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a956e32b176d645db54db3c86586cc0bfa2fbd3c iuc parents: 20 diff changeset	558 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
18 d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	559 </test>
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	560 </tests>
8 2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	561
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	562 <help><![CDATA[
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	563 featureCounts
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	564 #############
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	565
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	566 Overview
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	567 --------
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	568 FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. FeatureCounts is part of the Subread_ package.
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	569
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	570 Input formats
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	571 -------------
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	572 Alignments should be provided in either:
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	573
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	574 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	575 - BAM format
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	576
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	577 Annotations for gene regions should be provided in the GFF/GTF format:
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	578
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	579 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	580 - http://www.ensembl.org/info/website/upload/gff.html
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	581
14 85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	582 Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotation files are in simplified annotation format (SAF) as shown below. The GeneID column contains Entrez gene identifiers and each entry (row) is taken as a feature (e.g. an exon).
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	583
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	584 Example - Built-in annotation format:
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	585
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	586 ====== ==== ======= ======= ======
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	587 GeneID Chr Start End Strand
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	588 ====== ==== ======= ======= ======
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	589 497097 chr1 3204563 3207049 -
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	590 497097 chr1 3411783 3411982 -
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	591 497097 chr1 3660633 3661579 -
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	592 ====== ==== ======= ======= ======
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	593
15 a8dc8dabf0f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e10bdc912c2628796487886c00b70318a6214c5e iuc parents: 14 diff changeset	594 These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy annotateMyIDs tool.
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	595
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	596 Output format
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	597 -------------
13 386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	598 FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC.
10 46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	599
14 85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	600 .. _Subread: http://subread.sourceforge.net/
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	601 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
85aaf50ad9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	602 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
0 9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	603 ]]></help>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	604 <citations>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	605 <citation type="doi">10.1093/bioinformatics/btt656</citation>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	606 </citations>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	607 </tool>

Mercurial > repos > iuc > featurecounts

annotate featurecounts.xml @ 24:a37612abf7f9 draft