Mercurial > repos > yhoogstrate > featurecounts

annotate featurecounts.xml @ 3:e04fbcc4e91a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
author yhoogstrate
date Wed, 07 Oct 2015 11:38:41 -0400
parents b5c93611d2c5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
1 <tool id="featurecounts" name="featureCounts" version="1.4.6.p5">
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
3 <requirements>
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
4 <requirement type="package" version="1.4.6.p5">featurecounts</requirement>
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
5 </requirements>
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
6 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
7 <command><![CDATA[
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
8
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
9 ## Check 01: do the alignments have a dbkey and is the option set to using it?
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
10 #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
11 echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
12 #else
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
13 ## Check 02: are all alignments from the same type (bam || sam)
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
14 #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
15 echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
16 #else
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
17 featureCounts
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
18 -a
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
19 #if $reference_gene_sets_source.source_select == "indexed_filtered"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
20 "$reference_gene_sets_source.reference_gene_sets"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
21 #else if $reference_gene_sets_source.source_select == "indexed_all"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
22 "$reference_gene_sets_source.reference_gene_sets"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
23 #else if $reference_gene_sets_source.source_select == "history"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
24 "$reference_gene_sets_source.reference_gene_sets"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
25 #else
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
26 #*
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
27 This is a workaround to obtain the "genome.fa" file that
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
28 corresponds to the dbkey of the alignments.
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
29 Because this file is "calculated" during run-time, it can
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
30 be used in a workflow.
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
31 *#
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
32 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
33 #end if
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
34
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
35 -o "${output}"
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
36 -T \${GALAXY_SLOTS:-2}
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
37
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
38 #if $extended_parameters.parameters == "extended"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
39 -t $extended_parameters.gff_feature_type
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
40 -g $extended_parameters.gff_feature_attribute
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
41 $extended_parameters.summarization_level
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
42 $extended_parameters.contribute_to_multiple_features
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
43 $extended_parameters.protocol
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
44 $extended_parameters.multimapping_counts
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
45 -Q $extended_parameters.mapping_quality
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
46 $extended_parameters.fragment_counting
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
47 $extended_parameters.check_distance
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
48 -d $extended_parameters.minimum_fragment_length
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
49 -D $extended_parameters.maximum_fragment_length
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
50 $extended_parameters.only_both_ends
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
51 $extended_parameters.exclude_chimerics
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
52 #end if
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
53
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
54 #for $alignment in $alignments
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
55 ${alignment}
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
56 #end for
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
57
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
58 2>&1
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
59
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
60 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)]
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
61 #set $columns=",".join($columns)
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
62
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
63 #if $format == "tabdel_default" or $format.value == "tabdel_default"
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
64 && cp $output tmp.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
65 && egrep -v "^#" tmp.txt > tmp2.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
66 && cut -f 1,$columns tmp2.txt > tmp_left.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
67 && cut -f 6 tmp2.txt > tmp_right.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
68 && paste tmp_left.txt tmp_right.txt > $output
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
69 #elif $format == "tabdel_short" or $format.value == "tabdel_short"
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
70 && cp $output tmp.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
71 && egrep -v "^#" tmp.txt | cut -f 1,$columns > $output
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
72 #end if
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
73
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
74 ## For every alignment, replace its filename for: "hid: sample name"
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
75 #for $alignment in $alignments
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
76 #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.')
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
77 #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/')
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
78
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
79 #if $format.value == "tabdel_default" or $format.value == "tabdel_short"
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
80 && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
81 #elif $format.value == "bed":
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
82 && $__tool_directory__/featurecounts2bed.sh -f "$output" > tmp.txt
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
83 #else
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
84 && sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
85 #end if
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
86
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
87 && mv tmp.txt "${output}"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
88
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
89 && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
90 && mv tmp.txt ${output}".summary"
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
91 #end for
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
92 && mv ${output}".summary" "${output_summary}"
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
93 #end if
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
94 #end if
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
95 ]]></command>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
96 <inputs>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
97 <param name="alignments" type="data" format="bam,sam" label="Alignment file" 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 in the series must be in THE SAME format." multiple="true" />
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
98
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
99 <!-- Find out how to access the the GTF/GFF file(s) -->
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
100 <conditional name="reference_gene_sets_source">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
101 <param name="source_select" type="select" label="GFF/GTF Source">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
102 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
103 <option value="history">Use reference from the history</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
104 <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
105 <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
106 </param>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
107 <when value="indexed_filtered">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
108 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
109 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
110 <column name="name" index="0"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
111 <column name="dbkey" index="1"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
112 <column name="value" index="2"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
113 <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
114 <validator type="no_options" message="No indexes are available for the selected input dataset" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
115 </options>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
116 </param>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
117 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
118 <when value="history">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
119 <param name="reference_gene_sets" format="gff" type="data" label="Gene annotation file" help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment." />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
120 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
121 <when value="indexed_all">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
122 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
123 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
124 <column name="name" index="0"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
125 <column name="dbkey" index="1"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
126 <column name="value" index="2"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
127 <validator type="no_options" message="No indexes are available for the selected input dataset" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
128 </options>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
129 </param>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
130 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
131 <when value="attribute">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
132 <!-- Do nothing, determine GTF/GFF file at runtime -->
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
133 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
134 </conditional>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
135 <param name="format" type="select" label="Output format">
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
136 <option value="tabdel_default">Gene-name "\t" gene-count "\t" gene-length</option>
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
137 <option value="tabdel_short" selected="true">Gene-name "\t" gene-count</option>
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
138 <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount</option>
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
139 <option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
140 </param>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
141 <conditional name="extended_parameters">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
142 <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
143 <option value="default">Default settings</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
144 <option value="extended">Extended settings</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
145 </param>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
146 <when value="default">
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
147 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
148 <when value="extended">
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
149 <param name="gff_feature_type" type="text" value="exon"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
150 label="GFF feature type filter"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
151 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." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
152
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
153 <param name="gff_feature_attribute" type="text" value="gene_id"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
154 label="GFF gene identifier"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
155 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." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
156
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
157 <param name ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue=""
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
158 label="Allow read to contribute to multiple features"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
159 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
160
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
161 <param name="protocol" type="select" label="Strand specific protocol"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
162 help="Indicate if strand-specific read counting should be performed.">
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
163 <option value=" -s 0" selected="true">Unstranded</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
164 <option value=" -s 1">Stranded (forwards)</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
165 <option value=" -s 2">Stranded (reverse)</option>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
166 </param>
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
167
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
168 <param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue=""
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
169 label="Count multi-mapping reads/fragments"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
170 help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
171
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
172 <param name="mapping_quality" type="integer" value="12" label="Minimum read quality"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
173 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
174
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
175 <param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" checked="true"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
176 label="PE: Count fragments instead of reads"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
177 help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
178
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
179 <param name="check_distance" type="boolean" truevalue=" -P" falsevalue=""
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
180 label="PE: Check paired-end distance"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
181 help="Paired-end specific: If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
182
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
183 <param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
184 <param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." />
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
185
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
186 <param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue=""
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
187 label="PE: only allow fragments with both reads aligned"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
188 help="Paired-end specific: If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
189
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
190 <param name="exclude_chimerics" type="boolean" truevalue=" -C" falsevalue="" checked="true"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
191 label="PE: Exclude chimeric fragments"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
192 help="Paired-end specific: 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." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
193
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
194 <param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue=""
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
195 label="On feature level"
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
196 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." />
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
197
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
198 </when>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
199 </conditional>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
200 </inputs>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
201 <outputs>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
202 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
203 <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
204 </outputs>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
205 <tests>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
206 <test>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
207 <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
208 <param name="source_select" value="history" />
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
209 <param name="format" value="tabdel_default" />
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
210 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
211 <output name="output" file="output.tab"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
212 <output name="output_summary" file="output_summary.tab"/>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
213 </test>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
214 </tests>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
215
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
216 <help><![CDATA[
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
217 featureCounts
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
218 #############
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
219
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
220 Overview
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
221 --------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
222 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.
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
223 It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1].
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
224
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
225 Input formats
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
226 -------------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
227 Alignments should be provided in either:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
228
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
229 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
230 - BAM format
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
231
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
232 Gene regions should be provided in the GFF/GTF format:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
233
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
234 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
235 - http://www.ensembl.org/info/website/upload/gff.html
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
236
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
237 Installation
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
238 ------------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
239
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
240 1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
241
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
242 2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at: https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
243
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
244 License
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
245 -------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
246
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
247 **featureCounts / subread package**:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
248
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
249 - GNU General Public License version 3.0 (GPLv3)
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
250
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
251 Contact
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
252 -------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
253
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
254 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
255 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
256 Research IT (TraIT) project:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
257
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
258 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
259
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
260 More tools by the Translational Research IT (TraIT) project can be found
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
261 in the following toolsheds:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
262
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
263 http://toolshed.g2.bx.psu.edu/
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
264
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
265 http://testtoolshed.g2.bx.psu.edu/
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
266
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
267 References
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
268 ----------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
269 **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.**
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
270
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
271 *Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30.
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
272
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
273 - http://www.ncbi.nlm.nih.gov/pubmed/24227677
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
274 - http://dx.doi.org/10.1093/bioinformatics/btt656
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
275
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
276
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
277 Acknowledgements
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
278 ----------------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
279
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
280 I would like to thank Marius van den Beek for his contribution to this galaxy wrapper.
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
281 ]]></help>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
282 <citations>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
283 <citation type="doi">10.1093/bioinformatics/btt656</citation>
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
284 </citations>
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
285 </tool>