Mercurial > repos > bgruening > hicexplorer_hicdifferentialtad
view hicDifferentialTAD.xml @ 0:c852ad97ba28 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
author | bgruening |
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date | Tue, 16 Mar 2021 21:17:26 +0000 |
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children | 608538d083a2 |
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<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <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" /> <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" /> </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>