Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
comparison hicCorrectMatrix.xml @ 8:9a7d2fde825d draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
| author | iuc |
|---|---|
| date | Wed, 03 Jan 2018 13:21:17 -0500 |
| parents | bb0e8afdee82 |
| children | e1e5b2c47c00 |
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| 7:23df0dbb9b12 | 8:9a7d2fde825d |
|---|---|
| 1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> |
| 2 <description>Runs Dekker's iterative correction over a hic matrix.</description> | 2 <description>Runs Dekker's iterative correction over a hic matrix.</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicCorrectMatrix</token> | 4 <token name="@BINARY@">hicCorrectMatrix</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 18 #end if | 18 #end if |
| 19 | 19 |
| 20 #if $mode.mode_selector == 'correct': | 20 #if $mode.mode_selector == 'correct': |
| 21 | 21 |
| 22 --iterNum $mode.iterNum | 22 --iterNum $mode.iterNum |
| 23 #if $mode.outputFormat == 'h5' | 23 --outFileName matrix.$mode.outputFormat |
| 24 --outFileName matrix.h5 | |
| 25 #elif $mode.outputFormat == 'cool' | |
| 26 --outFileName matrix.cool | |
| 27 #end if | |
| 28 | 24 |
| 29 #if $mode.filterThreshold_low and $mode.filterThreshold_large: | 25 #if $mode.filterThreshold_low and $mode.filterThreshold_large: |
| 30 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large | 26 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large |
| 31 #end if | 27 #end if |
| 32 | 28 |
| 58 --plotName diagnostic_plot.png | 54 --plotName diagnostic_plot.png |
| 59 #if $mode.xMax: | 55 #if $mode.xMax: |
| 60 --xMax $mode.xMax | 56 --xMax $mode.xMax |
| 61 #end if | 57 #end if |
| 62 #end if | 58 #end if |
| 63 | 59 #if $mode.mode_selector == 'correct': |
| 60 && mv matrix.$mode.outputFormat matrix | |
| 61 #end if | |
| 64 ]]> | 62 ]]> |
| 65 </command> | 63 </command> |
| 66 <inputs> | 64 <inputs> |
| 67 <expand macro='matrix_h5_cooler_macro' /> | 65 <expand macro='matrix_h5_cooler_macro' /> |
| 68 <conditional name="mode"> | 66 <conditional name="mode"> |
| 112 </param> | 110 </param> |
| 113 </repeat> | 111 </repeat> |
| 114 | 112 |
| 115 </inputs> | 113 </inputs> |
| 116 <outputs> | 114 <outputs> |
| 117 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5"> | 115 <data name="outFileName" from_work_dir="matrix" format="h5"> |
| 118 <filter>outputFormat == 'h5'</filter> | 116 <change_format> |
| 117 <when input="mode.outputFormat" value="cool" format="cool" /> | |
| 118 </change_format> | |
| 119 <filter>mode['mode_selector'] == "correct"</filter> | 119 <filter>mode['mode_selector'] == "correct"</filter> |
| 120 | 120 |
| 121 </data> | 121 </data> |
| 122 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool"> | 122 |
| 123 <filter>outputFormat == 'cool'</filter> | |
| 124 <filter>mode['mode_selector'] == "correct"</filter> | |
| 125 | |
| 126 </data> | |
| 127 | 123 |
| 128 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> | 124 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> |
| 129 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> | 125 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> |
| 130 </data> | 126 </data> |
| 131 </outputs> | 127 </outputs> |