Mercurial > repos > iuc > featurecounts
changeset 6:9d60a36b5c6a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
| author | iuc |
|---|---|
| date | Thu, 26 Oct 2017 15:11:19 -0400 |
| parents | de2c5e5a206c |
| children | 3ce1c701b0df |
| files | featurecounts.xml test-data/output_1_summary.tab test-data/output_2_summary.tab |
| diffstat | 3 files changed, 60 insertions(+), 34 deletions(-) [+] |
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--- a/featurecounts.xml Wed Feb 15 06:11:21 2017 -0500 +++ b/featurecounts.xml Thu Oct 26 15:11:19 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="featurecounts" name="featureCounts" version="1.4.6.p5" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.5.3" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> - <requirement type="package" version="1.4.6p5">subread</requirement> + <requirement type="package" version="1.5.3">subread</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> @@ -9,16 +9,16 @@ ## Check whether all alignments are from the same type (bam || sam) featureCounts #if $gtf_source.ref_source=="history": - -a "$gtf_source.reference_gene_sets" + -a '$gtf_source.reference_gene_sets' #else: - -a "$gtf_source.reference_gene_sets_builtin.fields.path" + -a '$gtf_source.reference_gene_sets_builtin.fields.path' #end if -o "output" -T \${GALAXY_SLOTS:-2} - -t "$extended_parameters.gff_feature_type" - -g "$extended_parameters.gff_feature_attribute" + -t '$extended_parameters.gff_feature_type' + -g '$extended_parameters.gff_feature_attribute' $extended_parameters.summarization_level $extended_parameters.contribute_to_multiple_features -s $extended_parameters.strand_specificity @@ -28,6 +28,13 @@ $extended_parameters.multimapping_enabled.fraction #end if + $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads + #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J" + -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' + #end if + + $extended_parameters.long_reads + -Q $extended_parameters.mapping_quality $extended_parameters.largest_overlap --minOverlap $extended_parameters.min_overlap @@ -53,10 +60,9 @@ #end if $pe_parameters.only_both_ends - -S $pe_parameters.orientation $pe_parameters.exclude_chimerics - "${alignment}" + '${alignment}' ## Removal of comment and column-header line && grep -v "^#" "output" | tail -n+2 > body.txt @@ -69,19 +75,23 @@ ## Thus the gene length column (last column) has to be added separately && cut -f 6 body.txt > gene_lengths.txt && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak - && mv -f expression_matrix.txt.bak "${output_medium}" + && mv -f expression_matrix.txt.bak '${output_medium}' #elif $format.value == "tabdel_short" - && cut -f 1,7 body.txt > "${output_short}" + && cut -f 1,7 body.txt > '${output_short}' #else - && cp body.txt "${output_full}" + && cp body.txt '${output_full}' #end if #if str($include_feature_length_file) == "true" - && cut -f 1,6 body.txt > "${output_feature_lengths}" + && cut -f 1,6 body.txt > '${output_feature_lengths}' #end if - && tail -n+2 "output.summary" > "${output_summary}" + #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J" + && tail -n+2 'output.jcounts' > '${output_jcounts}' + #end if + + && tail -n+2 'output.summary' > '${output_summary}' ]]></command> <inputs> @@ -180,16 +190,6 @@ label="Only allow fragments with both reads aligned" help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." /> - <param name="orientation" - type="select" - label="Orientation of the two read from the same pair" - argument="-S" - help="Default is 'fr'"> - <option value="fr" selected="true">Forward, Reverse (fr)</option> - <option value="ff">Forward, Forward (ff)</option> - <option value="rf">Reverse, Forward (rf)</option> - </param> - <param name="exclude_chimerics" type="boolean" truevalue=" -C" @@ -269,6 +269,22 @@ label="Minimum mapping quality per read" 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." /> + <conditional name="exon_exon_junction_read_counting_enabled"> + <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" + label="Exon-exon junctions" + help="If specified, reads supporting each exon-exon junction will be counted" /> + <when value="-J"> + <param name="genome" argument="-G" type="data" format="fasta" + label="Reference sequence (genome) file" + help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" /> + </when> + <when value="" /> + </conditional> + + <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" + label="Long reads" + help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." /> + <param name="largest_overlap" type="boolean" truevalue=" --largestOverlap" @@ -373,11 +389,19 @@ <data format="tabular" name="output_feature_lengths" label="${tool.name} on ${on_string}: feature lengths"> - <filter>include_feature_length_file</filter> + <filter>include_feature_length_file</filter> <actions> <action name="column_names" type="metadata" default="Feature,Length" /> </actions> </data> + + <data name="output_jcounts" format="tabular" + label="${tool.name} on ${on_string}: junction counts"> + <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter> + <actions> + <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" /> + </actions> + </data> </outputs> <tests> <test>
--- a/test-data/output_1_summary.tab Wed Feb 15 06:11:21 2017 -0500 +++ b/test-data/output_1_summary.tab Thu Oct 26 15:11:19 2017 -0400 @@ -1,11 +1,12 @@ Assigned 158 -Unassigned_Ambiguity 0 -Unassigned_MultiMapping 0 -Unassigned_NoFeatures 6078 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 +Unassigned_Chimera 0 Unassigned_FragmentLength 0 -Unassigned_Chimera 0 +Unassigned_Duplicate 0 +Unassigned_MultiMapping 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 -Unassigned_Duplicate 0 +Unassigned_NoFeatures 6078 +Unassigned_Overlapping_Length 0 +Unassigned_Ambiguity 0
--- a/test-data/output_2_summary.tab Wed Feb 15 06:11:21 2017 -0500 +++ b/test-data/output_2_summary.tab Thu Oct 26 15:11:19 2017 -0400 @@ -1,11 +1,12 @@ Assigned 158 -Unassigned_Ambiguity 0 -Unassigned_MultiMapping 0 -Unassigned_NoFeatures 6078 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 +Unassigned_Chimera 0 Unassigned_FragmentLength 0 -Unassigned_Chimera 0 +Unassigned_Duplicate 0 +Unassigned_MultiMapping 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 -Unassigned_Duplicate 0 +Unassigned_NoFeatures 6078 +Unassigned_Overlapping_Length 0 +Unassigned_Ambiguity 0