Mercurial > repos > bgruening > hicexplorer_hicdifferentialtad
view hicDifferentialTAD.xml @ 5:4977f65da0ff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author | iuc |
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date | Thu, 05 Dec 2024 18:30:32 +0000 |
parents | 5dfba24d7bdd |
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<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>searches for differential TADs</description> <macros> <token name="@BINARY@">hicDifferentialTAD</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$matrix_h5_cooler_target' 'matrix_target.$matrix_h5_cooler_target.ext' && ln -s '$matrix_h5_cooler_control' 'matrix_control.$matrix_h5_cooler_control.ext' && @BINARY@ --targetMatrix 'matrix_target.$matrix_h5_cooler_target.ext' --controlMatrix 'matrix_control.$matrix_h5_cooler_control.ext' #if $tadDomains: --tadDomains '$tadDomains' #end if #if $pValue: --pValue $pValue #end if --mode $mode_selector --modeReject $modeReject --outFileNamePrefix galaxy_differential_tad --threads @THREADS@ ]]> </command> <inputs> <param name="matrix_h5_cooler_target" type="data" format="h5,cool" label="Target matrix to compute on" /> <param name="matrix_h5_cooler_control" type="data" format="h5,cool" label="Control matrix to compute on" /> <param argument="--tadDomains" type="data" format="bed" optional="false" label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> <param argument="--pValue" type="float" label="P-value" min="0.0" max="1.0" help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value="0.05" /> <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression"> <option value="intra-TAD">intra-TAD</option> <option value="left-inter-TAD">left-inter-TAD</option> <option value="right-inter-TAD">right-inter-TAD</option> <option value="all" selected="True">all</option> </param> <param name="modeReject" type="select" label="Method to compute the differentail TAD expression"> <option value="one" selected="True">one</option> <option value="all">all</option> </param> </inputs> <outputs> <data name="acceptedTADs" from_work_dir="galaxy_differential_tad_accepted.diff_tad" format="txt" label="Accepted TADs" /> <data name="rejectedTADs" from_work_dir="galaxy_differential_tad_rejected.diff_tad" format="txt" label="Rejected TADs" /> </outputs> <tests> <test> <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" /> <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" /> <param name="tadDomains" ftype="bed" value="hicDifferentialTAD/multiNone_domains.bed" /> <param name="pValue" value="1.0" /> <param name="mode_selector" value="all" /> <param name="modeReject" value="one" /> <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" /> <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes--> <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" lines_diff="4"/> </test> </tests> <help><![CDATA[ Differential TAD detection ========================== Computes if precomputed TADs are differentially expressed between two samples. 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>