Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 20:f5a37c3906cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
author iuc
date Tue, 10 Jan 2023 18:37:39 +0000
parents e4cb7809df61
children ea19190ce5e0
comparison
equal deleted inserted replaced
19:e4cb7809df61 20:f5a37c3906cc
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>
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 cp '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10 10
11 @BINARY@ 11 @BINARY@
12 $mode.mode_selector 12 $mode.mode_selector
13 --matrix 'matrix.$matrix_h5_cooler.ext' 13 --matrix 'matrix.$matrix_h5_cooler.ext'
14 14
53 --xMax $mode.xMax 53 --xMax $mode.xMax
54 #end if 54 #end if
55 $mode.perchr 55 $mode.perchr
56 #end if 56 #end if
57 #if $mode.mode_selector == 'correct': 57 #if $mode.mode_selector == 'correct':
58 && mv matrix.$matrix_h5_cooler.ext matrix 58 && mv matrix.$matrix_h5_cooler.ext '$outFileName'
59 #end if 59 #end if
60 ]]> 60 ]]>
61 </command> 61 </command>
62 <inputs> 62 <inputs>
63 <expand macro='matrix_h5_cooler_macro' /> 63 <expand macro='matrix_h5_cooler_macro' />
66 <option value="diagnostic_plot">Diagnostic plot</option> 66 <option value="diagnostic_plot">Diagnostic plot</option>
67 <option value="correct">Correct matrix</option> 67 <option value="correct">Correct matrix</option>
68 </param> 68 </param>
69 <when value="diagnostic_plot"> 69 <when value="diagnostic_plot">
70 <expand macro="xMax" /> 70 <expand macro="xMax" />
71 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" /> 71 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
72 </when> 72 </when>
73 <when value="correct"> 73 <when value="correct">
74 <conditional name='correctionMethod'> 74 <conditional name='correctionMethod'>
75 <param name='correctionMethod_selector' type='select' label='Correction method'> 75 <param name='correctionMethod_selector' type='select' label='Correction method'>
76 <option value='ice'>Iterative_correction (Imakaev)</option> 76 <option value='ice'>Iterative_correction (Imakaev)</option>
77 <option value='kr'>Knights-Ruiz</option> 77 <option value='kr'>Knights-Ruiz</option>
78 </param> 78 </param>
79 79
80 <when value='ice'> 80 <when value='ice'>
81 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" /> 81 <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
82 82
83 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. 83 <param argument="--inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." /> 84 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." />
85 85
86 <param argument="--transCutoff" name="transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." /> 86 <param argument="--transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." />
87 87
88 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads. 88 <param argument="--sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads.
89 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." /> 89 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." />
90 90
91 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" /> 91 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
92 92
93 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" /> 93 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
94 <expand macro="filterThreshold" /> 94 <expand macro="filterThreshold" />
95 </when> 95 </when>
96 <when value='kr'> 96 <when value='kr'>
97 </when> 97 </when>
98 </conditional> 98 </conditional>
106 </param> 106 </param>
107 </repeat> 107 </repeat>
108 108
109 </inputs> 109 </inputs>
110 <outputs> 110 <outputs>
111 <data name="outFileName" from_work_dir="matrix" format="cool"> 111 <data name="outFileName" format="cool">
112 <change_format> 112 <change_format>
113 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" /> 113 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
114 </change_format> 114 </change_format>
115 <filter>mode['mode_selector'] == "correct"</filter> 115 <filter>mode['mode_selector'] == "correct"</filter>
116 </data> 116 </data>
117 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> 117 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot">
118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> 118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
119 </data> 119 </data>
120 </outputs> 120 </outputs>
121 <tests> 121 <tests>
122 <test> 122 <test>