Mercurial > repos > bgruening > hicexplorer_hicinterintratad
view hicInterIntraTAD.xml @ 0:55b013e59018 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author | bgruening |
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date | Wed, 18 Oct 2023 17:02:07 +0000 |
parents | |
children | c261b6b05ee3 |
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<tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>computes the ratio of inter TAD-scores vs. intra TADs</description> <macros> <token name="@BINARY@">hicInterIntraTAD</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext' --tadDomains '$tadDomains' #if $fontSize: --fontSize $fontSize #end if #if $dpi: --dpi $dpi #end if --outFileName output_interintra.txt --outFileNameRatioPlot plot.$image_file_format --threads @THREADS@ && mv plot.$image_file_format plot ]]> </command> <inputs> <expand macro="matrix_h5_cooler_macro" /> <param name="tadDomains" type="data" format="bed" label="Bed file with TAD domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." /> <expand macro="dpi" /> <param name="fontSize" type="integer" min="5" optional="True" label="Font size" help="Font size for 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> <option value="pdf">pdf</option> </param> </inputs> <outputs> <data name='output_txt' from_work_dir='output_interintra.txt' format='txt' label='Intra Inter TAD ratios'/> <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> <change_format> <when input="image_file_format" value="svg" format="svg" /> <when input="image_file_format" value="pdf" format="pdf" /> </change_format> </data> </outputs> <tests> <test> <param name="matrix_h5_cooler" value="hicInterIntraTAD/matrix.cool" /> <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" /> <output name="output_txt" file="hicInterIntraTAD/output.txt" ftype="txt" /> <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" /> </test> </tests> <help><![CDATA[ Calculate the ratio of inter-TAD contacts vs intra-TADs ======================================================= Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs. This tool supports to compute the ratio of contacts of a TAD (intra-TAD) with the contacts outside of it (inter-TAD). For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html ]]> </help> <expand macro="citations" /> </tool>