Mercurial > repos > yhoogstrate > featurecounts

comparison featurecounts.xml @ 2:b5c93611d2c5 draft

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 b05640a41e2106782ac7f88f858b0a256918fa6f
author yhoogstrate
date Thu, 10 Sep 2015 05:11:49 -0400
parents 63bd455ed299
children e04fbcc4e91a
comparison
equal deleted inserted replaced
1:63bd455ed299 2:b5c93611d2c5
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="featurecounts" name="featureCounts" version="1.4.6.p1"> 2 <tool id="featurecounts" name="featureCounts" version="1.4.6.p1">
3 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> 3 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.4.6.p1">featurecounts</requirement> 5 <requirement type="package" version="1.4.6.p1">featurecounts</requirement>
6 <requirement type="package" version="1.0.0">featurecounts2bed</requirement> 6 <requirement type="package" version="1.0.0">featurecounts2bed</requirement>
7 </requirements> 7 </requirements>
8 <version_command>featureCounts -v</version_command> 8 <version_command>featureCounts -v</version_command>
9 <command> 9 <command><![CDATA[
10 #* 10 ## Check 01: do the alignments have a dbkey and is the option set to using it?
11 The following script is written in the "Cheetah" language: 11
12 http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html 12 #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
13 *# 13 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
14 14 #else
15 ## Check 01: do the alignments have a dbkey and is the option set to using it? 15 ## Check 02: are all alignments from the same type (bam || sam)
16 #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 16 #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1
17 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!" >&amp;2 17 echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2
18 #else 18 #else
19 ## Check 02: are all alignments from the same type (bam || sam) 19 featureCounts
20 #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1 20 -a
21 echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&amp;2 21 #if $reference_gene_sets_source.source_select == "indexed_filtered"
22 #else 22 "$reference_gene_sets_source.reference_gene_sets"
23 featureCounts 23 #else if $reference_gene_sets_source.source_select == "indexed_all"
24 -a 24 "$reference_gene_sets_source.reference_gene_sets"
25 #if $reference_gene_sets_source.source_select == "indexed_filtered" 25 #else if $reference_gene_sets_source.source_select == "history"
26 "$reference_gene_sets_source.reference_gene_sets" 26 "$reference_gene_sets_source.reference_gene_sets"
27 #else if $reference_gene_sets_source.source_select == "indexed_all" 27 #else
28 "$reference_gene_sets_source.reference_gene_sets" 28 #*
29 #else if $reference_gene_sets_source.source_select == "history" 29 This is a workaround to obtain the "genome.fa" file that
30 "$reference_gene_sets_source.reference_gene_sets" 30 corresponds to the dbkey of the alignments.
31 #else 31 Because this file is "calculated" during run-time, it can
32 #* 32 be used in a workflow.
33 This is a workaround to obtain the "genome.fa" file that 33 *#
34 corresponds to the dbkey of the alignments. 34 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
35 Because this file is "calculated" during run-time, it can 35 #end if
36 be used in a workflow. 36
37 *# 37 -o "$output"
38 "${ 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] }" 38 -T \${GALAXY_SLOTS:-2}
39 #end if 39
40 40 #if $extended_parameters.parameters == "extended"
41 -o "$output" 41 -t $extended_parameters.gff_feature_type
42 -T \${GALAXY_SLOTS:-2} 42 -g $extended_parameters.gff_feature_attribute
43 43 $extended_parameters.summarization_level
44 #if $extended_parameters.parameters == "extended" 44 $extended_parameters.contribute_to_multiple_features
45 -t $extended_parameters.gff_feature_type 45 $extended_parameters.protocol
46 -g $extended_parameters.gff_feature_attribute 46 $extended_parameters.multimapping_counts
47 $extended_parameters.summarization_level 47 -Q $extended_parameters.mapping_quality
48 $extended_parameters.contribute_to_multiple_features 48 $extended_parameters.fragment_counting
49 $extended_parameters.protocol 49 $extended_parameters.check_distance
50 $extended_parameters.multimapping_counts 50 -d $extended_parameters.minimum_fragment_length
51 -Q $extended_parameters.mapping_quality 51 -D $extended_parameters.maximum_fragment_length
52 $extended_parameters.fragment_counting 52 $extended_parameters.only_both_ends
53 $extended_parameters.check_distance 53 $extended_parameters.exclude_chimerics
54 -d $extended_parameters.minimum_fragment_length 54 $extended_parameters.namesort
55 -D $extended_parameters.maximum_fragment_length 55 #end if
56 $extended_parameters.only_both_ends 56
57 $extended_parameters.exclude_chimerics 57 #for $alignment in $alignments
58 $extended_parameters.namesort 58 ${alignment}
59 #end if 59 #end for
60 60
61 #for $alignment in $alignments 61 2>&1
62 ${alignment} 62
63 #end for 63 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)]
64 64 #set $columns=",".join($columns)
65 2>&amp;1 65
66 66 #if $format == "tabdel_default" or $format.value == "tabdel_default"
67 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] 67 ; cp $output tmp.txt
68 #set $columns=",".join($columns) 68 ; egrep -v "^#" tmp.txt > tmp2.txt
69 69 ; cut -f 1,$columns tmp2.txt > tmp_left.txt
70 #if $format == "tabdel_default" or $format.value == "tabdel_default" 70 ; cut -f 6 tmp2.txt > tmp_right.txt
71 ; cp $output tmp.txt 71 ; paste tmp_left.txt tmp_right.txt > $output
72 ; egrep -v "^#" tmp.txt > tmp2.txt 72 #elif $format == "tabdel_short" or $format.value == "tabdel_short"
73 ; cut -f 1,$columns tmp2.txt > tmp_left.txt 73 ; cp $output tmp.txt
74 ; cut -f 6 tmp2.txt > tmp_right.txt 74 ; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output
75 ; paste tmp_left.txt tmp_right.txt > $output 75 #end if
76 #elif $format == "tabdel_short" or $format.value == "tabdel_short" 76
77 ; cp $output tmp.txt 77 ## For every alignment, replace its filename for: "hid: sample name"
78 ; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output 78 #for $alignment in $alignments
79 #end if 79 #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.')
80 80 #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/')
81 ## For every alignment, replace its filename for: "hid: sample name" 81
82 #for $alignment in $alignments 82 #if $format.value == "tabdel_default" or $format.value == "tabdel_short"
83 #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.') 83 ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
84 #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/') 84 #elif $format.value == "bed":
85 85 ; featurecounts2bed.sh -f "$output" > tmp.txt
86 #if $format.value == "tabdel_default" or $format.value == "tabdel_short" 86 #else
87 ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt 87 ; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
88 #elif $format.value == "bed": 88 #end if
89 ; featurecounts2bed.sh -f "$output" > tmp.txt 89
90 #else 90 ; mv tmp.txt $output
91 ; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt 91
92 #end if 92 ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt
93 93 ; mv tmp.txt $output".summary"
94 ; mv tmp.txt $output 94 #end for
95 95 ; mv $output".summary" $output_summary
96 ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt 96 #end if
97 ; mv tmp.txt $output".summary" 97 #end if
98 #end for 98 ]]></command>
99 ; mv $output".summary" $output_summary 99
100 #end if 100 <inputs>
101 #end if 101 <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" />
102 </command> 102
103 103 <!-- Find out how to access the the GTF/GFF file(s) -->
104 <inputs> 104 <conditional name="reference_gene_sets_source">
105 <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" /> 105 <param name="source_select" type="select" label="GFF/GTF Source">
106 106 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
107 <!-- Find out how to access the the GTF/GFF file(s) --> 107 <option value="history">Use reference from the history</option>
108 <conditional name="reference_gene_sets_source"> 108 <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
109 <param name="source_select" type="select" label="GFF/GTF Source"> 109 <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
110 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> 110 </param>
111 <option value="history">Use reference from the history</option> 111 <when value="indexed_filtered">
112 <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> 112 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
113 <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> 113 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
114 </param> 114 <column name="name" index="0"/>
115 <when value="indexed_filtered"> 115 <column name="dbkey" index="1"/>
116 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > 116 <column name="value" index="2"/>
117 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> 117 <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
118 <column name="name" index="0"/> 118 <validator type="no_options" message="No indexes are available for the selected input dataset" />
119 <column name="dbkey" index="1"/> 119 </options>
120 <column name="value" index="2"/> 120 </param>
121 <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" /> 121 </when>
122 <validator type="no_options" message="No indexes are available for the selected input dataset" /> 122 <when value="history">
123 </options> 123 <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." />
124 </param> 124 </when>
125 </when> 125 <when value="indexed_all">
126 <when value="history"> 126 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
127 <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." /> 127 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
128 </when> 128 <column name="name" index="0"/>
129 <when value="indexed_all"> 129 <column name="dbkey" index="1"/>
130 <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > 130 <column name="value" index="2"/>
131 <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> 131 <validator type="no_options" message="No indexes are available for the selected input dataset" />
132 <column name="name" index="0"/> 132 </options>
133 <column name="dbkey" index="1"/> 133 </param>
134 <column name="value" index="2"/> 134 </when>
135 <validator type="no_options" message="No indexes are available for the selected input dataset" /> 135 <when value="attribute">
136 </options> 136 <!-- Do nothing, determine GTF/GFF file at runtime -->
137 </param> 137 </when>
138 </when> 138 </conditional>
139 <when value="attribute"> 139
140 <!-- Do nothing, determine GTF/GFF file at runtime --> 140 <param name="format" type="select" label="Output format">
141 </when> 141 <option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option>
142 </conditional> 142 <option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option>
143 143 <option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option>
144 <param name="format" type="select" label="Output format"> 144 <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option>
145 <option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option> 145 </param>
146 <option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option> 146
147 <option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option> 147 <conditional name="extended_parameters">
148 <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option> 148 <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
149 </param> 149 <option value="default">Default settings</option>
150 150 <option value="extended">Extended settings</option>
151 <conditional name="extended_parameters"> 151 </param>
152 <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings."> 152 <when value="default">
153 <option value="default">Default settings</option> 153 </when>
154 <option value="extended">Extended settings</option> 154 <when value="extended">
155 </param> 155 <param name="gff_feature_type" type="text" value="exon" 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." />
156 <when value="default"> 156
157 </when> 157 <param name="gff_feature_attribute" type="text" value="gene_id" 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." />
158 <when value="extended"> 158
159 <param name="gff_feature_type" type="text" value="exon" 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." /> 159 <param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue="" 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." />
160 160
161 <param name="gff_feature_attribute" type="text" value="gene_id" 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." /> 161 <param name ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue="" label="Allow read to contribute to multiple features" 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)" />
162 162
163 <param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue="" 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." /> 163 <param name="protocol" type="select" label="Strand specific protocol" help="Indicate if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.">
164 164 <option value=" -s 0" selected="true">Unstranded</option>
165 <param name ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue="" label="Allow read to contribute to multiple features" 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)" /> 165 <option value=" -s 1">Stranded (forwards)</option>
166 166 <option value=" -s 2">Stranded (reverse)</option>
167 <param name="protocol" type="select" label="Strand specific protocol" help="Indicate if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default."> 167 </param>
168 <option value=" -s 0" selected="true">Unstranded</option> 168
169 <option value=" -s 1">Stranded (forwards)</option> 169 <param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" 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." />
170 <option value=" -s 2">Stranded (reverse)</option> 170
171 </param> 171 <param name="mapping_quality" type="integer" value="0" label="Minimum read quality" 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." />
172 172
173 <param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" 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." /> 173 <param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" label="PE: Count fragments instead of reads" help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads. The two reads from the same fragment must be adjacent to each other in the provided SAM/BAM file. If SAM/BAM input does not meet this requirement, the -S (sorting) option should be provided as well." />
174 174
175 <param name="mapping_quality" type="integer" value="0" label="Minimum read quality" 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." /> 175 <param name="check_distance" type="boolean" truevalue=" -P" falsevalue="" label="PE: Check paired-end distance" 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." />
176 176
177 <param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" label="PE: Count fragments instead of reads" help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads. The two reads from the same fragment must be adjacent to each other in the provided SAM/BAM file. If SAM/BAM input does not meet this requirement, the -S (sorting) option should be provided as well." /> 177 <param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." />
178 178 <param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." />
179 <param name="check_distance" type="boolean" truevalue=" -P" falsevalue="" label="PE: Check paired-end distance" 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." /> 179
180 180 <param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue="" label="PE: only allow fragments with both reads aligned" 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." />
181 <param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." /> 181
182 <param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." /> 182 <param name="exclude_chimerics" type="boolean" truevalue=" -C" falsevalue="" label="PE: Exclude chimeric fragments" 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." />
183 183
184 <param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue="" label="PE: only allow fragments with both reads aligned" 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." /> 184 <param name="namesort" type="boolean" truevalue=" -S" falsevalue="" label="PE: Name-sort reads (slow!)" help="Paired-end specific: If specified, the program will reorder input reads according to their names and make reads from the same pair be adjacent to each other. This option should be provided when reads from the same pair are not adjacent to each other in input SAM/BAM files (for instance sorting reads by chromosomal locations could decouple reads from the same pair)." />
185 185 </when>
186 <param name="exclude_chimerics" type="boolean" truevalue=" -C" falsevalue="" label="PE: Exclude chimeric fragments" 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." /> 186 </conditional>
187 187 </inputs>
188 <param name="namesort" type="boolean" truevalue=" -S" falsevalue="" label="PE: Name-sort reads (slow!)" help="Paired-end specific: If specified, the program will reorder input reads according to their names and make reads from the same pair be adjacent to each other. This option should be provided when reads from the same pair are not adjacent to each other in input SAM/BAM files (for instance sorting reads by chromosomal locations could decouple reads from the same pair)." /> 188
189 </when> 189 <outputs>
190 </conditional> 190 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
191 </inputs> 191 <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
192 192 </outputs>
193 <outputs> 193
194 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> 194 <tests>
195 <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> 195 <test>
196 </outputs> 196 <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" />
197 197 <param name="source_select" value="history" />
198 <tests> 198 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
199 <test> 199 <output name="output" file="output.tab"/>
200 <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" /> 200 <output name="output_summary" file="output_summary.tab"/>
201 <param name="source_select" value="history" /> 201 </test>
202 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 202 </tests>
203 <output name="output" file="output.tab"/> 203
204 <output name="output_summary" file="output_summary.tab"/> 204 <help><![CDATA[
205 </test>
206 </tests>
207
208 <help>
209 featureCounts 205 featureCounts
210 ############# 206 #############
211 207
212 Overview 208 Overview
213 -------- 209 --------
250 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch 246 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
251 247
252 More tools by the Translational Research IT (TraIT) project can be found 248 More tools by the Translational Research IT (TraIT) project can be found
253 in the following toolsheds: 249 in the following toolsheds:
254 250
255 http://toolshed.dtls.nl/
256
257 http://toolshed.g2.bx.psu.edu/ 251 http://toolshed.g2.bx.psu.edu/
258 252
259 http://testtoolshed.g2.bx.psu.edu/ 253 http://testtoolshed.g2.bx.psu.edu/
260 254
261 References 255 References
269 263
270 264
271 Acknowledgements 265 Acknowledgements
272 ---------------- 266 ----------------
273 267
274 I would like to thank Marius van den Beek for his contributions to this project. 268 I would like to thank Marius van den Beek for his contribution to this galaxy wrapper.
275 </help> 269 ]]></help>
276 <citations> 270 <citations>
277 <citation type="doi">10.1093/bioinformatics/btt656</citation> 271 <citation type="doi">10.1093/bioinformatics/btt656</citation>
278 </citations> 272 </citations>
279 </tool> 273 </tool>