Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
changeset 20:f5a37c3906cc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
| author | iuc |
|---|---|
| date | Tue, 10 Jan 2023 18:37:39 +0000 |
| parents | e4cb7809df61 |
| children | ea19190ce5e0 |
| files | hicCorrectMatrix.xml macros.xml |
| diffstat | 2 files changed, 13 insertions(+), 13 deletions(-) [+] |
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--- a/hicCorrectMatrix.xml Tue Mar 16 15:41:08 2021 +0000 +++ b/hicCorrectMatrix.xml Tue Jan 10 18:37:39 2023 +0000 @@ -6,7 +6,7 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && + cp '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && @BINARY@ $mode.mode_selector @@ -55,7 +55,7 @@ $mode.perchr #end if #if $mode.mode_selector == 'correct': - && mv matrix.$matrix_h5_cooler.ext matrix + && mv matrix.$matrix_h5_cooler.ext '$outFileName' #end if ]]> </command> @@ -68,7 +68,7 @@ </param> <when value="diagnostic_plot"> <expand macro="xMax" /> - <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" /> + <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" /> </when> <when value="correct"> <conditional name='correctionMethod'> @@ -78,19 +78,19 @@ </param> <when value='ice'> - <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" /> + <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" /> - <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. + <param argument="--inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." /> - <param argument="--transCutoff" name="transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." /> + <param argument="--transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." /> - <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads. + <param argument="--sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads. A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." /> - <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" /> + <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" /> - <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" /> + <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" /> <expand macro="filterThreshold" /> </when> <when value='kr'> @@ -108,13 +108,13 @@ </inputs> <outputs> - <data name="outFileName" from_work_dir="matrix" format="cool"> + <data name="outFileName" format="cool"> <change_format> <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" /> </change_format> <filter>mode['mode_selector'] == "correct"</filter> </data> - <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> + <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot"> <filter>mode['mode_selector'] == "diagnostic_plot"</filter> </data> </outputs>
--- a/macros.xml Tue Mar 16 15:41:08 2021 +0000 +++ b/macros.xml Tue Jan 10 18:37:39 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." />