Mercurial > repos > iuc > featurecounts
changeset 8:2a8bb8223a45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
| author | iuc |
|---|---|
| date | Wed, 15 Nov 2017 15:53:25 -0500 |
| parents | 3ce1c701b0df |
| children | e6a2a912677a |
| files | featurecounts.xml |
| diffstat | 1 files changed, 41 insertions(+), 14 deletions(-) [+] |
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--- a/featurecounts.xml Mon Oct 30 14:49:13 2017 -0400 +++ b/featurecounts.xml Wed Nov 15 15:53:25 2017 -0500 @@ -1,7 +1,7 @@ -<tool id="featurecounts" name="featureCounts" version="1.5.3" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.6.0" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> - <requirement type="package" version="1.5.3">subread</requirement> + <requirement type="package" version="1.6.0">subread</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> @@ -37,9 +37,13 @@ $extended_parameters.long_reads + $extended_parameters.by_read_group + -Q $extended_parameters.mapping_quality $extended_parameters.largest_overlap --minOverlap $extended_parameters.min_overlap + --fracOverlap $extended_parameters.frac_overlap + --fracOverlapFeature $extended_parameters.frac_overlap_feature $extended_parameters.read_reduction $extended_parameters.primary $extended_parameters.ignore_dup @@ -83,7 +87,7 @@ #else && cp body.txt '${output_full}' #end if - + #if str($include_feature_length_file) == "true" && cut -f 1,6 body.txt > '${output_feature_lengths}' @@ -103,7 +107,7 @@ 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 must be in the same format" /> - + <conditional name="gtf_source"> <param name="ref_source" type="select" label="Gene annotation file"> <option value="cached">locally cached</option> @@ -125,7 +129,7 @@ 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" /> </when> </conditional> - + <param name="format" type="select" label="Output format" @@ -134,7 +138,7 @@ <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option> <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option> </param> - + <param name="include_feature_length_file" type="boolean" truevalue="true" @@ -183,7 +187,7 @@ </when> <when value="" /> </conditional> - + <param name="only_both_ends" type="boolean" truevalue=" -B" @@ -201,7 +205,7 @@ label="Exclude chimeric fragments" help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." /> </section> - + <section name="extended_parameters" title="Advanced options"> <param name="gff_feature_type" type="text" @@ -287,6 +291,11 @@ 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="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue="" + label="Count reads by read group" + help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." /> + + <param name="largest_overlap" type="boolean" truevalue=" --largestOverlap" @@ -299,9 +308,27 @@ type="integer" value="1" argument="--minOverlap" - label="Minimum overlap" + label="Minimum bases of overlap" help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." /> + <param name="frac_overlap" + type="integer" + value="0" + min="0" + max="1" + argument="--fracOverlap" + label="Minimum fraction (of read) overlapping a feature" + help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." /> + + <param name="frac_overlap_feature" + type="integer" + value="0" + min="0" + max="1" + argument="--fracOverlapFeature" + label="Minimum fraction (of feature) overlapping a read" + help="Specify the minimum required fraction of bases included in a feature overlapping bases between a read (or a read-pair). Value should be within range [0,1]. 0 by default." /> + <param name="read_extension_5p" type="integer" value="0" @@ -325,7 +352,7 @@ <option value="--read2pos 5">Reduce it to the 5' end</option> <option value="--read2pos 3">Reduce it to the 3' end</option> </param> - + <param name="primary" type="boolean" truevalue=" --primary" @@ -333,7 +360,7 @@ argument="--primary" label="Only count primary alignments" help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." /> - + <param name="ignore_dup" type="boolean" truevalue=" --ignoreDup" @@ -341,7 +368,7 @@ argument="--ignoreDup" label="Ignore reads marked as duplicate" help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> - + <param name="count_split_alignments_only" type="boolean" truevalue=" --countSplitAlignmentsOnly" @@ -452,9 +479,9 @@ <metadata name="column_names" value="Feature,Length"/> </output> </test> - + </tests> - + <help><![CDATA[ featureCounts #############