Mercurial > repos > bgruening > hicexplorer_chicqualitycontrol
diff chicQualityControl.xml @ 6:db4a82804126 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:23:20 +0000 |
| parents | 0e149d0c112c |
| children | b892fa1fcaec |
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--- a/chicQualityControl.xml Fri Dec 11 21:31:00 2020 +0000 +++ b/chicQualityControl.xml Tue Mar 16 15:23:20 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>generates an estimate of the quality of each viewpoint</description> <macros> <token name="@BINARY@">chicQualityControl</token> @@ -13,7 +13,6 @@ #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) @BINARY@ - --matrices $m --referencePoints '$referencePoints' --sparsity $sparsity @@ -26,18 +25,14 @@ && mv histogram.$image_file_format histogram && mv sparsity.$image_file_format sparsity - ]]></command> + ]]> </command> <inputs> <expand macro="matrix_h5_cooler_multiple_macro" /> + <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." /> + <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help='Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix.' /> + <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' /> - <param argument="--referencePoints" type="data" format='interval' - label="Reference points" - help="Bed file contains all reference points which should be used to build the background model." /> - <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help='Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix.'/> - - <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/> - - <param name='dpi' type='integer' value='300' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> + <param name='dpi' type='integer' value='300' min="100" max="2000" optional='true' label='DPI for image' help='Change the default resolution of the plot.' /> <param name="image_file_format" type="select" label="Image output format"> <option value="png" selected="True">png</option> <option value="svg">svg</option> @@ -46,13 +41,13 @@ </inputs> <outputs> - <data name="raw_reference_points" from_work_dir="reference_points_raw_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points raw"/> - <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points rejected"/> - <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points accepted"/> - <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points failed"/> - - <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report"/> - + <data name="raw_reference_points" from_work_dir="reference_points_raw_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points raw" /> + <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points rejected" /> + <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points accepted" /> + <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points failed" /> + + <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report" /> + <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot"> <change_format> <when input="image_file_format" value="svg" format="svg" /> @@ -68,18 +63,18 @@ </outputs> <tests> <test> - <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> - <param name="referencePoints" value="cHi-C/referencePoints.bed"/> - <param name='sparsity' value='0.05'/> + <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" /> + <param name="referencePoints" value="cHi-C/referencePoints.bed" /> + <param name='sparsity' value='0.05' /> - <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" compare="sim_size" delta='40000'/> - <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" compare="sim_size" delta='40000'/> - <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" compare="sim_size" delta='40000'/> - <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" compare="sim_size" delta='40000'/> - <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" compare="sim_size" delta='40000'/> - - <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' delta='40000'/> - <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" delta='40000'/> + <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" /> + <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" /> + <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" /> + <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" /> + <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" /> + + <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' /> + <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" /> </test> </tests> @@ -99,6 +94,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>