Mercurial > repos > bgruening > hicexplorer_hicfindtads

comparison hicFindTADs.xml @ 14:1d9b575fe97d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 06:51:50 -0400
parents 6b7987d22eab
children d404277cc87a
comparison
equal deleted inserted replaced
13:d3fad161b318 14:1d9b575fe97d
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && 9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10 10
11 #if $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed': 11 #if $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed':
12 ln -s '$precomputedZscore_conditional.scoreFile' 'prefix_tad_score.bm' && 12 ln -s '$precomputedZscore_conditional.scoreFile' 'prefix_tad_score.bm' &&
13 ln -s '$precomputedZscore_conditional.zscoreMatrix' 'prefix_zscore_matrix.h5' && 13 ln -s '$precomputedZscore_conditional.zscoreMatrix' 'prefix_zscore_matrix.h5' &&
14 #end if 14 #end if
15 @BINARY@ 15 @BINARY@
16 --matrix 'matrix.$matrix_h5_cooler.ext' 16 --matrix 'matrix.$matrix_h5_cooler.ext'
17 17
70 <when value='precomputed'> 70 <when value='precomputed'>
71 <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)"/> 71 <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)"/>
72 <param name="zscoreMatrix" type="data" format='h5' label="Precomputed z-score matrix"/> 72 <param name="zscoreMatrix" type="data" format='h5' label="Precomputed z-score matrix"/>
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 75
76 <conditional name="multiple_comparison_conditional"> 76 <conditional name="multiple_comparison_conditional">
77 <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" > 77 <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" >
78 <option value="fdr" selected="True">False discovery rate</option> 78 <option value="fdr" selected="True">False discovery rate</option>
79 <option value="bonferroni">Bonferroni correction</option> 79 <option value="bonferroni">Bonferroni correction</option>
80 <option value="None">No correction</option> 80 <option value="None">No correction</option>
135 <param name="precomputedZscore_selector" value="scratch"/> 135 <param name="precomputedZscore_selector" value="scratch"/>
136 <param name="minDepth" value="15000"/> 136 <param name="minDepth" value="15000"/>
137 <param name="maxDepth" value="30000"/> 137 <param name="maxDepth" value="30000"/>
138 <param name="step" value="15000"/> 138 <param name="step" value="15000"/>
139 </conditional> 139 </conditional>
140 140
141 <param name="minBoundaryDistance" value="5000" /> 141 <param name="minBoundaryDistance" value="5000" />
142 <conditional name="multiple_comparison_conditional"> 142 <conditional name="multiple_comparison_conditional">
143 <param name="multiple_comparison_selector" value="fdr"/> 143 <param name="multiple_comparison_selector" value="fdr"/>
144 <param name="threshold" value="0.8" /> 144 <param name="threshold" value="0.8" />
145 </conditional> 145 </conditional>