Mercurial > repos > lparsons > bam_to_bigwig
changeset 5:5b40b93ebae3 default tip
Added advanced settings
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Wed, 24 Aug 2011 16:44:28 -0400 |
| parents | 3112c78841c5 |
| children | |
| files | bam_to_bigwig.xml |
| diffstat | 1 files changed, 18 insertions(+), 1 deletions(-) [+] |
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--- a/bam_to_bigwig.xml Wed Aug 24 14:45:29 2011 -0400 +++ b/bam_to_bigwig.xml Wed Aug 24 16:44:28 2011 -0400 @@ -8,7 +8,11 @@ genomeCoverageBed -ibam $align -bg $split -g `awk '($0 !~ /^#.*/) && ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai > tmp.bedgraph; - bedGraphToBigWig tmp.bedgraph + bedGraphToBigWig + #if $settings.settingsType == "full": + -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc} + #end if + tmp.bedgraph `awk '($0 !~ /^#.*/) && ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai $out; </command> @@ -18,6 +22,19 @@ <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> </param> <param name="split" type="boolean" value="false" label="Separate split reads" help="Do not use gaps when computing coverage. This is recommended for RNA-Seq where reads are mapped across long splice junctions. Uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage." truevalue="-split" falsevalue="" /> + <conditional name="settings"> + <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used."> + <option value="preset">Default</option> + <option value="full">Full parameter list</option> + </param> + <when value="preset" /> + <when value="full"> + <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" /> + <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" /> + <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/> + </when> + </conditional> + </inputs> <outputs> <data format="bigwig" name="out" />