Mercurial > repos > yhoogstrate > featurecounts_valid_gff
changeset 41:c55c0c51b634
Uploaded
author | yhoogstrate |
---|---|
date | Fri, 28 Feb 2014 07:26:46 -0500 |
parents | 4850787ee1d9 |
children | 70292f11ba10 |
files | featurecounts_valid_gff.xml |
diffstat | 1 files changed, 22 insertions(+), 6 deletions(-) [+] |
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--- a/featurecounts_valid_gff.xml Mon Feb 24 08:19:34 2014 -0500 +++ b/featurecounts_valid_gff.xml Fri Feb 28 07:26:46 2014 -0500 @@ -76,6 +76,20 @@ ; cp $output tmp.txt ; egrep -v "^#" tmp.txt | cut -f 1,7 > $output #end if + + ## For every alignment, replace its filename for: "hid: sample name" + #for $alignment in $alignments + #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.') + #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/') + + #if $format == "tabdel_default" or $format.value == "tabdel_default" or $format == "tabdel_short" or $format.value == "tabdel_short" + ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt + #else + ; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt + #end if + + ; mv tmp.txt $output + #end for #end if #end if </command> @@ -102,6 +116,9 @@ </options> </param> </when> + <when value="history"> + <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 annotaiton file corresponds to the same reference genome as used for the alignment." /> + </when> <when value="indexed_all"> <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> @@ -112,9 +129,6 @@ </options> </param> </when> - <when value="history"> - <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 annotaiton file corresponds to the same reference genome as used for the alignment." /> - </when> <when value="attribute"> <!-- Do nothing, determine GTF/GFF file at runtime --> </when> @@ -176,7 +190,6 @@ <help> featureCounts-valid-gff:: - **Overview** 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. @@ -192,8 +205,9 @@ * http://genome.ucsc.edu/FAQ/FAQformat.html#format3 * http://www.ensembl.org/info/website/upload/gff.html -FeatureCounts is only able to handle the UCSC variant. Therefore the project was forked to "featureCounts-valid-gff", able to handle both. -Whis wrapper wraps the fork, such that it is independent of the GFF/GTF variant. +FeatureCounts is only able to handle the UCSC GFF/GTF variant. Therefore the project was forked to "featureCounts-valid-gff", able to handle both. +Whis wrapper wraps the fork, such that it is independent of the GFF/GTF variant. The URL of the fork is: +https://code.google.com/p/featurecounts-valid-gff/ **Input formats** @@ -225,6 +239,8 @@ The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch +I want to thank the Marius van den Beek for his contribution as well. + More tools by the Translational Research IT (TraIT) project can be found in the following repository: http://toolshed.nbic.nl/