featurecounts: featurecounts.xml annotate

annotate featurecounts.xml @ 37:8620533d294b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c43e4b51d4b0a46eeba363fa4061d4af03a677a4

author	iuc
date	Wed, 07 May 2025 09:59:13 +0000
parents	39863c075dca
children

rev	line source
37 8620533d294b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c43e4b51d4b0a46eeba363fa4061d4af03a677a4 iuc parents: 36 diff changeset	1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
30 56aa64c23690 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 29 diff changeset	2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
28 db82f928d25e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786" iuc parents: 27 diff changeset	3 <macros>
37 8620533d294b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c43e4b51d4b0a46eeba363fa4061d4af03a677a4 iuc parents: 36 diff changeset	4 <token name="@TOOL_VERSION@">2.1.1</token>
35 519ae9e6fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit eb563889f227d5c473e2bad2cf9a513e41d03fca iuc parents: 34 diff changeset	5 <token name="@VERSION_SUFFIX@">0</token>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	6 <macro name="conditional_gff_opions">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	7 <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" 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."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	8 <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" 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. Ex: if the 9th column is 'gene_id "ENSG00000223972"; gene_name "DDX11L1" gene_source "havana"' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	9 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" label="On feature level" 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."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	10 </macro>
28 db82f928d25e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786" iuc parents: 27 diff changeset	11 </macros>
30 56aa64c23690 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 29 diff changeset	12 <xrefs>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	13 <xref type="bio.tools">featurecounts</xref>
30 56aa64c23690 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 29 diff changeset	14 </xrefs>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	15 <requirements>
28 db82f928d25e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786" iuc parents: 27 diff changeset	16 <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
35 519ae9e6fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit eb563889f227d5c473e2bad2cf9a513e41d03fca iuc parents: 34 diff changeset	17 <requirement type="package" version="1.21">samtools</requirement>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	18 </requirements>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	19
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	20 <version_command>featureCounts -v 2>&1 \| grep .</version_command>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	21 <command detect_errors="exit_code"><![CDATA[
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	22 ## Export fc path for its built-in annotation
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	23 export FC_PATH=\$(command -v featureCounts \| sed 's@/bin/featureCounts$@@') &&
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	24
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	25 ## Check whether all alignments are from the same type (bam \|\| sam)
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	26 featureCounts
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	27
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	28 #if $anno.anno_select=="history":
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	29 -a '$anno.reference_gene_sets'
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	30 -F "GTF"
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	31 #elif $anno.anno_select=="cached":
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	32 -a '$anno.reference_gene_sets_cached.fields.path'
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	33 -F "GTF"
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	34 #elif $anno.anno_select=="builtin":
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	35 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	36 -F "SAF"
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	37 #end if
711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	38
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	39 -o "output"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	40 -T \${GALAXY_SLOTS:-2}
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	41
14 786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	42 -s $strand_specificity
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	43
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	44 -Q $read_filtering_parameters.mapping_quality
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	45 $read_filtering_parameters.splitonly
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	46 $read_filtering_parameters.primary
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	47 $read_filtering_parameters.ignore_dup
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	48
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	49 #if $anno.anno_select!="builtin":
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	50 -t '$anno.gff_feature_type'
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	51 -g '$anno.gff_feature_attribute'
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	52 $anno.summarization_level
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	53 #end if
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	54
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	55 $extended_parameters.multifeatures.multifeat
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	56 #if $extended_parameters.multifeatures.multifeat != "":
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	57 $extended_parameters.multifeatures.fraction
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	58 #end if
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	59
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	60 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	61 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	62 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
7 889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	63 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	64 #end if
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	65 #end if
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	66
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	67 $extended_parameters.long_reads
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	68
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	69 $extended_parameters.by_read_group
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	70
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	71 $extended_parameters.largest_overlap
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	72 --minOverlap $extended_parameters.min_overlap
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	73 --fracOverlap $extended_parameters.frac_overlap
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	74 --fracOverlapFeature $extended_parameters.frac_overlap_feature
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	75 $extended_parameters.read_reduction
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	76 #if $extended_parameters.R:
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	77 $extended_parameters.R
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	78 #end if
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	79 #if str($extended_parameters.read_extension_5p) != "0":
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	80 --readExtension5 $extended_parameters.read_extension_5p
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	81 #end if
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	82
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	83 #if str($extended_parameters.read_extension_3p) != "0":
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	84 --readExtension3 $extended_parameters.read_extension_3p
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	85 #end if
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	86
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	87 #if str($pe_parameters.paired_end_status) != "single_end":
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	88 -p
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	89 $pe_parameters.only_both_ends
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	90 $pe_parameters.exclude_chimerics
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	91 #if str($pe_parameters.paired_end_status) == "PE_fragments":
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	92 --countReadPairs
33 dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	93 #if $pe_parameters.check_distance_enabled.checkFragLength == "true":
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	94 --checkFragLength
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	95 --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	96 --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	97 #end if
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	98 #end if
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	99 #end if
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	100
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	101 '${alignment}'
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	102
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	103 ## Remove comment and add sample name to header
c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	104 && grep -v "^#" "output"
c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	105 \| sed -e 's\|${alignment}\|${alignment.element_identifier}\|g'
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	106 > body.txt
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	107 ## Set the right columns for the tabular formats
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	108 #if $format.value == "tabdel_medium":
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	109 && cut -f 1,7 body.txt > expression_matrix.txt
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	110
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	111 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	112 ## Thus the gene length column (last column) has to be added separately
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	113 && cut -f 6 body.txt > gene_lengths.txt
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	114 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	115 && mv -f expression_matrix.txt.bak '${output_medium}'
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	116 #elif $format.value == "tabdel_short":
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	117 && cut -f 1,7 body.txt > '${output_short}'
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	118 #else:
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	119 && cp body.txt '${output_full}'
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	120 #end if
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	121
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	122 #if str($include_feature_length_file) == "true":
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	123 && cut -f 1,6 body.txt > '${output_feature_lengths}'
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	124 #end if
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	125
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	126 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	127 && sed -e 's\|${alignment}\|${alignment.element_identifier}\|g' 'output.jcounts' > '${output_jcounts}'
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	128 #end if
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	129
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	130 #if $extended_parameters.R:
28 db82f928d25e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786" iuc parents: 27 diff changeset	131 && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	132 #end if
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	133 && sed -e 's\|${alignment}\|${alignment.element_identifier}\|g' 'output.summary' > '${output_summary}'
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	134 ]]></command>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	135 <inputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	136 <param name="alignment"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	137 type="data"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	138 multiple="false"
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	139 format="unsorted.bam,bam,sam"
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	140 label="Alignment file"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	141 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 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	142 </param>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	143
14 786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	144 <param name="strand_specificity"
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	145 type="select"
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	146 label="Specify strand information"
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	147 argument="-s"
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	148 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)">
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	149 <option value="0" selected="true">Unstranded</option>
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	150 <option value="1">Stranded (Forward)</option>
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	151 <option value="2">Stranded (Reverse)</option>
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	152 </param>
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	153
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	154 <conditional name="anno">
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	155 <param name="anno_select" type="select" label="Gene annotation file">
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	156 <option value="builtin">featureCounts built-in</option>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	157 <option value="cached" selected="True">locally cached</option>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	158 <option value="history">A GFF/GTF file in your history</option>
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	159 </param>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	160 <when value="builtin">
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	161 <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">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	162 <options from_data_table="featurecounts_anno">
25 9f24599f93e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 24 diff changeset	163 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	164 <filter type="sort_by" column="1"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	165 </options>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	166 <validator type="no_options" message="An built-in annotation file is not available for the genome build associated with the selected input file"/>
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	167 </param>
711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	168 </when>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	169 <when value="cached">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	170 <param name="reference_gene_sets_cached" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator.">
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	171 <options from_data_table="gene_sets">
25 9f24599f93e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08" iuc parents: 24 diff changeset	172 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	173 <filter type="sort_by" column="2"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	174 </options>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	175 <validator type="no_options" message="A cached annotation file is not available for the genome build associated with the selected input file"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	176 </param>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	177 <expand macro="conditional_gff_opions"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	178 </when>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	179 <when value="history">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	180 <param name="reference_gene_sets"
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	181 format="gff,gtf,gff3"
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	182 type="data"
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	183 label="Gene annotation file"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	184 help="The program assumes that the provided annotation file is in GFF/GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment.">
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	185 </param>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	186 <expand macro="conditional_gff_opions"/>
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	187 </when>
711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	188 </conditional>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	189
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	190 <param name="format"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	191 type="select"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	192 label="Output format"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	193 help="The output format will be tabular, select the preferred columns here">
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	194 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	195 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	196 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	197 </param>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	198
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	199 <param name="include_feature_length_file"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	200 type="boolean"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	201 truevalue="true"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	202 falsevalue="false"
2 4d0763d3eb93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2d5ab40b214e429d8a9d0c5b2b35adfc46a87e6 iuc parents: 1 diff changeset	203 checked="false"
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	204 label="Create gene-length file"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	205 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"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	206
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	207 <conditional name="pe_parameters">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	208 <param name="paired_end_status" type="select" label="Does the input have read pairs?" help="Were the bam files generated by aligning the output of a paired-end sequencing experiment? If yes, the tool can consider 2 reads = 1 read pair as 1 entity to count. Alternatively, you can opt to consider treating the read pairs as 2 individual reads to count seperately.">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	209 <option value="single_end" selected="True">No, single-end.</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	210 <option value="PE_individual">Yes, paired-end but still count them as if individual reads.</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	211 <option value="PE_fragments">Yes, paired-end and count them as 1 single fragment.</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	212 </param>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	213
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	214 <when value="single_end"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	215 <when value="PE_individual">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	216 <param name="only_both_ends"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	217 type="boolean"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	218 truevalue=" -B"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	219 falsevalue=""
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	220 argument="-B"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	221 label="Only allow fragments with both reads aligned"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	222 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."/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	223
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	224 <param name="exclude_chimerics"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	225 type="boolean"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	226 truevalue=" -C"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	227 falsevalue=""
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	228 argument="-C"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	229 checked="true"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	230 label="Exclude chimeric fragments"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	231 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."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	232 </when>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	233 <when value="PE_fragments">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	234 <conditional name="check_distance_enabled">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	235 <param argument="--checkFragLength" type="select" label="Check paired-end distance" 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 can be specified using -d and -D (minimum and maximum fragment/template length) options.">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	236 <option value="true">Check the distance between paired reads</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	237 <option value="false" selected="True">Do not check</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	238 </param>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	239 <when value="true">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	240 <param name="minimum_fragment_length"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	241 type="integer"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	242 value="50"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	243 min="0"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	244 argument="-d"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	245 label="Minimum fragment/template length."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	246 <param name="maximum_fragment_length"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	247 type="integer"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	248 value="600"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	249 min="1"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	250 argument="-D"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	251 label="Maximum fragment/template length."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	252 </when>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	253 <when value="false"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	254 </conditional>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	255
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	256 <param name="only_both_ends"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	257 type="boolean"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	258 truevalue=" -B"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	259 falsevalue=""
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	260 argument="-B"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	261 label="Only allow fragments with both reads aligned"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	262 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."/>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	263
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	264 <param name="exclude_chimerics"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	265 type="boolean"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	266 truevalue=" -C"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	267 falsevalue=""
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	268 argument="-C"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	269 checked="true"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	270 label="Exclude chimeric fragments"
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	271 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."/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	272 </when>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	273 </conditional>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	274
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	275 <section name="read_filtering_parameters" title="Read filtering options">
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	276 <param name="mapping_quality"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	277 type="integer"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	278 value="0"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	279 min="0"
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	280 argument="-Q"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	281 label="Minimum mapping quality per read"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	282 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."/>
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	283 <param name="splitonly" type="select" display="radio" label="Filter split alignments" help="Split alignments are alignments with CIGAR string containing 'N', e.g. exon spanning reads in RNASeq.">
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	284 <option value="">No filtering: count split and non-split alignments</option>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	285 <option value="--splitOnly">Count only split alignments (--splitOnly)</option>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	286 <option value="--nonSplitOnly">Count only non-split alignments (--nonSplitOnly)</option>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	287 </param>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	288 <param type="boolean"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	289 truevalue=" --primary"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	290 falsevalue=""
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	291 argument="--primary"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	292 label="Only count primary alignments"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	293 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)."/>
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	294 <param name="ignore_dup"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	295 type="boolean"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	296 truevalue=" --ignoreDup"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	297 falsevalue=""
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	298 argument="--ignoreDup"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	299 label="Ignore reads marked as duplicate"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	300 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."/>
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	301 </section>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	302
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	303 <section name="extended_parameters" title="Advanced options">
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	304 <conditional name = "multifeatures">
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	305 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction">
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	306 <option value="" selected="true">Disabled: reads that align to multiple features or overlapping features are excluded</option>
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	307 <option value="-M">Enabled: multi-mapping reads are included (-M)</option>
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	308 <option value="-O">Enabled: multi-overlapping features are included (-O)</option>
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	309 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	310 </param>
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	311 <when value=""/>
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	312 <when value="-M">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	313 <param type="boolean"
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	314 truevalue="--fraction"
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	315 falsevalue=""
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	316 argument="--fraction"
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	317 label="Assign fractions to multi-mapping reads"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	318 help="If specified, a fractional count 1/x will be generated for each multi-mapping read, where x is the number of alignments (indicated by 'NH' tag) reported for the read."/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	319 </when>
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	320 <when value="-O">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	321 <param type="boolean"
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	322 truevalue="--fraction"
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	323 falsevalue=""
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	324 argument="--fraction"
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	325 label="Assign fractions to multi-overlapping features"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	326 help="If specified, a fractional count 1/y will be generated for each multi-overlapping feature, where y is the number of features overlapping with the read."/>
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	327 </when>
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	328 <when value="-O -M">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	329 <param type="boolean"
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	330 truevalue="--fraction"
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	331 falsevalue=""
48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	332 argument="--fraction"
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	333 label="Assign fractions to both multi-mapping reads and multi-overlapping features"
83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	334 help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/>
26 48a5ee6c175c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4" iuc parents: 25 diff changeset	335 </when>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	336 </conditional>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	337
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	338 <conditional name="exon_exon_junction_read_counting_enabled">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	339 <param name="count_exon_exon_junction_reads" type="select" argument="-J" label="Exon-exon junctions" help="Junctions are identified from those exon-spanning reads (containing ‘N’ in CIGAR string) in input data. The output result includes names of primary and secondary genes that overlap at least one of the two splice sites of a junction.">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	340 <option value="-J">Count reads supporting each exon-exon junction.</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	341 <option value="" selected="True">Do not count</option>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	342 </param>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	343 <when value="-J">
7 889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	344 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	345 label="Reference sequence file"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	346 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions"/>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	347 </when>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	348 <when value=""/>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	349 </conditional>
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	350
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	351 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	352 label="Long reads"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	353 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."/>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	354
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	355 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	356 label="Count reads by read group"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	357 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files."/>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	358
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	359 <param name="largest_overlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	360 type="boolean"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	361 truevalue=" --largestOverlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	362 falsevalue=""
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	363 argument="--largestOverlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	364 label="Largest overlap"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	365 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	366
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	367 <param name="min_overlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	368 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	369 value="1"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	370 argument="--minOverlap"
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	371 label="Minimum bases of overlap"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	372 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."/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	373
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	374 <param name="frac_overlap"
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	375 type="integer"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	376 value="0"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	377 min="0"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	378 max="1"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	379 argument="--fracOverlap"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	380 label="Minimum fraction (of read) overlapping a feature"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	381 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."/>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	382
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	383 <param name="frac_overlap_feature"
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	384 type="integer"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	385 value="0"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	386 min="0"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	387 max="1"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	388 argument="--fracOverlapFeature"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	389 label="Minimum fraction (of feature) overlapping a read"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	390 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."/>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	391
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	392 <param name="read_extension_5p"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	393 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	394 value="0"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	395 min="0"
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	396 argument="--readExtension5"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	397 label="Read 5' extension"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	398 help="Reads are extended upstream by ... bases from their 5' end"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	399
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	400 <param name="read_extension_3p"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	401 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	402 value="0"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	403 min="0"
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	404 argument="--readExtension3"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	405 label="Read 3' extension"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	406 help="Reads are extended upstream by ... bases from their 3' end"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	407
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	408 <param name="read_reduction"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	409 type="select"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	410 label="Reduce read to single position"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	411 argument="--read2pos"
3 711c80e57384 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f iuc parents: 2 diff changeset	412 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 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	413 <option value="" selected="true">Leave the read as it is</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	414 <option value="--read2pos 5">Reduce it to the 5' end</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	415 <option value="--read2pos 3">Reduce it to the 3' end</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	416 </param>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	417
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	418 <param type="boolean"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	419 truevalue="-R BAM"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	420 falsevalue=""
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	421 argument="-R"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	422 label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	423 help=""/>
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	424
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	425 </section>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	426 </inputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	427 <outputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	428 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	429 name="output_medium"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	430 label="${tool.name} on ${on_string}: Counts (with length)">
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	431 <filter>format == "tabdel_medium"</filter>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	432 <actions>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	433 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	434 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	435 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	436
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	437 <data format="bam"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	438 name="output_bam"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	439 label="${tool.name} on ${on_string}: Alignment file">
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	440 <filter>extended_parameters['R']</filter>
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	441 </data>
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	442
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	443 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	444 name="output_short"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	445 label="${tool.name} on ${on_string}: Counts">
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	446 <filter>format == "tabdel_short"</filter>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	447 <actions>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	448 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	449 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	450 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	451
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	452 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	453 name="output_full"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	454 label="${tool.name} on ${on_string}: Counts (with location)">
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	455 <filter>format == "tabdel_full"</filter>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	456 <actions>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	457 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	458 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	459 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	460
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	461 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	462 name="output_summary"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	463 label="${tool.name} on ${on_string}: Summary">
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	464 <actions>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	465 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	466 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	467 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	468
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	469 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	470 name="output_feature_lengths"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	471 label="${tool.name} on ${on_string}: Feature lengths">
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	472 <filter>include_feature_length_file</filter>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	473 <actions>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	474 <action name="column_names" type="metadata" default="Feature,Length"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	475 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	476 </data>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	477
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	478 <data name="output_jcounts" format="tabular"
20 b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5 iuc parents: 19 diff changeset	479 label="${tool.name} on ${on_string}: Junction counts">
7 889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	480 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	481 <actions>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	482 <action name="column_names" type="metadata"
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	483 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}"/>
6 e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	484 </actions>
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b iuc parents: 4 diff changeset	485 </data>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	486 </outputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	487 <tests>
7 889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	488 <test expect_num_outputs="3">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	489 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	490 <param name="anno_select" value="history"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	491 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	492 <param name="format" value="tabdel_medium"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	493 <param name="include_feature_length_file" value="true"/>
4 2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	494 <output name="output_medium" file="output_1_medium.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	495 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	496 </output>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	497 <output name="output_summary" file="output_1_summary.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	498 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	499 </output>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	500 </test>
7 889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17 iuc parents: 6 diff changeset	501 <test expect_num_outputs="3">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	502 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	503 <param name="anno_select" value="history"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	504 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	505 <param name="format" value="tabdel_full"/>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	506 <param name="include_feature_length_file" value="true"/>
4 2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	507 <output name="output_full" file="output_1_full.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	508 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	509 </output>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	510 <output name="output_summary" file="output_1_summary.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	511 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	512 </output>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	513 <output name="output_feature_lengths" file="output_feature_lengths.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	514 <metadata name="column_names" value="Feature,Length"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04 iuc parents: 3 diff changeset	515 </output>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	516 </test>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	517 <test expect_num_outputs="4">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	518 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	519 <param name="anno_select" value="history"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	520 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	521 <param name="format" value="tabdel_short"/>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	522 <param name="include_feature_length_file" value="true"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	523 <param name="count_exon_exon_junction_reads" value="-J"/>
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	524 <output name="output_short" file="output_1_short.tab">
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	525 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	526 </output>
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	527 <output name="output_summary" file="output_1_summary.tab">
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	528 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	529 </output>
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	530 <output name="output_jcounts" file="output_1_jcounts.tab">
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	531 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	532 </output>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	533 </test>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	534 <!-- Ensure featureCounts built-in annotation works -->
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	535 <test expect_num_outputs="3">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	536 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	537 <param name="anno_select" value="builtin"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	538 <param name="format" value="tabdel_short"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	539 <conditional name="pe_parameters">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	540 <param name="paired_end_status" value="PE_individual"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	541 </conditional>
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	542 <section name="extended_parameters">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	543 <param name="R" value="true"/>
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	544 </section>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	545 <output name="output_short" file="output_builtin_hg19.tab">
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	546 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	547 </output>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	548 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
17 5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018 iuc parents: 15 diff changeset	549 <output name="output_bam" file="output.bam" ftype="bam"/>
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	550 </test>
33 dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	551 <!-- Ensure fragment counting works -->
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	552 <test expect_num_outputs="3">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	553 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
33 dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	554 <param name="anno_select" value="builtin"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	555 <param name="format" value="tabdel_short"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	556 <conditional name="pe_parameters">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	557 <param name="paired_end_status" value="PE_fragments"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	558 </conditional>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	559 <section name="extended_parameters">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	560 <param name="R" value="true"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	561 </section>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	562 <output name="output_short" file="output_builtin_hg19_fragment.tab">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	563 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	564 </output>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	565 <output name="output_summary" file="output_summary_builtin_hg19_fragments.tab"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	566 <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc iuc parents: 32 diff changeset	567 </test>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	568 <!-- Ensure cached GTFs work -->
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	569 <test expect_num_outputs="3">
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	570 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	571 <param name="anno_select" value="cached"/>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	572 <param name="format" value="tabdel_medium"/>
11 d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	573 <param name="include_feature_length_file" value="true"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	574 <output name="output_medium" file="output_1_medium.tab">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	575 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	576 </output>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	577 <output name="output_summary" file="output_1_summary.tab">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	578 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	579 </output>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb iuc parents: 10 diff changeset	580 </test>
18 34b78acbad1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	581 <!-- Ensure BAM output works -->
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	582 <test expect_num_outputs="3">
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	583 <param name="alignment" value="subset.sorted.bam" ftype="bam"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	584 <param name="anno_select" value="history"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	585 <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	586 <section name="extended_parameters">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	587 <param name="R" value="true"/>
18 34b78acbad1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	588 </section>
21 d4d69c4d0780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a956e32b176d645db54db3c86586cc0bfa2fbd3c iuc parents: 20 diff changeset	589 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
34 12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	590 <output name="output_short" file="subset.sorted.featurecounts_short.tab">
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	591 <metadata name="column_names" value="Geneid,subset.sorted.bam"/>
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	592 </output>
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 iuc parents: 33 diff changeset	593 <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/>
18 34b78acbad1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 iuc parents: 17 diff changeset	594 </test>
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	595 </tests>
8 bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41 iuc parents: 7 diff changeset	596
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	597 <help><![CDATA[
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	598 featureCounts
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	599 #############
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	600
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	601 Overview
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	602 --------
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	603 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 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	604
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	605 Input formats
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	606 -------------
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	607 Alignments should be provided in either:
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	608
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	609 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	610 - BAM format
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	611
10 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	612 Annotations for gene regions should be provided in the GFF/GTF format:
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	613
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	614 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	615 - http://www.ensembl.org/info/website/upload/gff.html
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	616
14 786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	617 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).
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	618
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	619 Example - Built-in annotation format:
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	620
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	621 ====== ==== ======= ======= ======
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	622 GeneID Chr Start End Strand
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	623 ====== ==== ======= ======= ======
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	624 497097 chr1 3204563 3207049 -
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	625 497098 chr1 3411783 3411982 -
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	626 497099 chr1 3660633 3661579 -
14 786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	627 ====== ==== ======= ======= ======
786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	628
35 519ae9e6fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit eb563889f227d5c473e2bad2cf9a513e41d03fca iuc parents: 34 diff changeset	629 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 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	630
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	631 Output format
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	632 -------------
13 c7085a3028ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4 iuc parents: 12 diff changeset	633 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 7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 iuc parents: 9 diff changeset	634
14 786a00071b49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca iuc parents: 13 diff changeset	635 .. _Subread: http://subread.sourceforge.net/
31 83ab9e468b86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13" iuc parents: 30 diff changeset	636 .. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
0 8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	637 ]]></help>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	638 <citations>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	639 <citation type="doi">10.1093/bioinformatics/btt656</citation>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	640 </citations>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: diff changeset	641 </tool>
32 456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 iuc parents: 31 diff changeset	642

Mercurial > repos > iuc > featurecounts

annotate featurecounts.xml @ 37:8620533d294b draft default tip