Mercurial > repos > bgruening > hicexplorer_hicfindtads
comparison hicFindTADs.xml @ 14:1d9b575fe97d draft
"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 |
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| 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> |