Mercurial > repos > bgruening > hicexplorer_hicconvertformat
changeset 7:2a24ce221cd7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
| author | iuc |
|---|---|
| date | Tue, 10 Jan 2023 19:02:29 +0000 |
| parents | 3e598b8e72e7 |
| children | c0737631eea1 |
| files | hicConvertFormat.xml macros.xml |
| diffstat | 2 files changed, 16 insertions(+), 13 deletions(-) [+] |
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--- a/hicConvertFormat.xml Tue Mar 16 15:38:11 2021 +0000 +++ b/hicConvertFormat.xml Tue Jan 10 19:02:29 2023 +0000 @@ -88,16 +88,8 @@ --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' - #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': - && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out - #else: - && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out - #end if - #end if - - ### Set up links to matrices to have correct ending - #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': + #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional #if $xml_path.inputFormat_selector == 'optionCool': @@ -206,6 +198,17 @@ --matrices $m #end if --outFileName matrix.mcool + #end if + $storeAppliedCorrection + $enforceInteger + + #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix': + #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': + && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out + #else: + && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out + #end if + #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': && mv matrix.mcool matrix_out #end if ]]> @@ -237,10 +240,10 @@ <expand macro='convertFormat_multiple_macro' /> </when> </conditional> - <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> - <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' /> </when> </conditional> + <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" /> + <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" /> </inputs> <outputs> <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
--- a/macros.xml Tue Mar 16 15:38:11 2021 +0000 +++ b/macros.xml Tue Jan 10 19:02:29 2023 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> <token name="@TOOL_VERSION@">3.6</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $use_range.range_min:$use_range.range_max @@ -333,7 +333,7 @@ <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" /> </xml> <xml name="xMax"> - <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" /> + <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" /> </xml> <xml name="filterThreshold"> <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />