Mercurial > repos > bgruening > deeptools_multi_bam_summary
changeset 6:b319edc108a7 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
| author | bgruening |
|---|---|
| date | Sun, 24 Apr 2016 16:21:06 -0400 |
| parents | f89672f49f94 |
| children | 87d2c75884d9 |
| files | deepTools_macros.xml multiBamSummary.xml test-data/bowtie2 test1.bam test-data/bowtie2-test1.bam test-data/plotCoverage_result1.tabular test-data/plotFingerprint_result2.tabular |
| diffstat | 6 files changed, 16 insertions(+), 10 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Mar 18 08:46:50 2016 -0400 +++ b/deepTools_macros.xml Sun Apr 24 16:21:06 2016 -0400 @@ -68,16 +68,22 @@ <xml name="region_limit_operation"> <param argument="--region" type="text" value="" label="Region of the genome to limit the operation to" - help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> + help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="|"/> + </valid> + </sanitizer> + </param> </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.2.2</token> + <token name="@WRAPPER_VERSION@">2.2.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.2.2">deepTools</requirement> + <requirement type="package" version="2.2.3">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -302,7 +308,7 @@ </token> <xml name="citations"> <citations> - <citation type="doi">10.1093/nar/gku365</citation> + <citation type="doi">10.1093/nar/gkw257</citation> <yield /> </citations> </xml>
--- a/multiBamSummary.xml Fri Mar 18 08:46:50 2016 -0400 +++ b/multiBamSummary.xml Sun Apr 24 16:21:06 2016 -0400 @@ -16,8 +16,8 @@ @THREADS@ --outFileName '$outFile' - --bamfiles '#echo "' '".join($files)#' - --labels '#echo "' '".join($labels)#' + --bamfiles #echo " ".join($files)# + --labels #echo " ".join($labels)# #if $outRawCounts: --outRawCounts '$outFileRawCounts' @@ -85,13 +85,13 @@ </outputs> <tests> <test> - <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" /> + <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> <param name="modeOpt" value="bins" /> <param name="binSize" value="10" /> <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> </test> <test> - <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" /> + <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> <param name="modeOpt" value="BED-file" /> <param name="region_file" value="multiBamSummary_regions.bed" /> <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
--- a/test-data/plotCoverage_result1.tabular Fri Mar 18 08:46:50 2016 -0400 +++ b/test-data/plotCoverage_result1.tabular Sun Apr 24 16:21:06 2016 -0400 @@ -1,4 +1,4 @@ -#'chr' 'start' 'end' 'bowtie2-test1.bam' 'bowtie2-test1.bam' +#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam' chrM 0 1 23.0 23.0 chrM 1 2 35.0 35.0 chrM 2 3 35.0 35.0