Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 7:1612e9458940 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:30:22 -0500
parents 44919af9194b
children f7d344dacfeb
comparison
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6:3889ecd44f20 7:1612e9458940
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>