Mercurial > repos > bgruening > hicexplorer_hicdifferentialtad
diff hicDifferentialTAD.xml @ 0:c852ad97ba28 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
author | bgruening |
---|---|
date | Tue, 16 Mar 2021 21:17:26 +0000 |
parents | |
children | 608538d083a2 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicDifferentialTAD.xml Tue Mar 16 21:17:26 2021 +0000 @@ -0,0 +1,81 @@ +<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>