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comparison hicCorrectMatrix.xml @ 0:d5bf8c60d661 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:21:47 -0400
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children ecf11dda45f7
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-1:000000000000 0:d5bf8c60d661
1 <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Runs Dekker's iterative correction over a hic matrix.</description>
3 <macros>
4 <token name="@BINARY@">hicCorrectMatrix</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 ln -s '$matrix' temp_matrix.npz.h5 &&
11
12 hicCorrectMatrix
13 $mode.mode_selector
14 --matrix temp_matrix.npz.h5
15
16 ## special: --chromosomes is optional, but if given needs at least one argument
17 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ])
18 #if chroms
19 --chromosomes "$chroms"
20 #end if
21
22 #if $mode.mode_selector == 'correct':
23
24 --iterNum $mode.iterNum
25 --outFileName corrected_matrix.npz.h5
26
27 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
28 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
29 #end if
30
31 #if $mode.inflationCutoff:
32 --inflationCutoff $mode.inflationCutoff
33 #end if
34
35 #if $mode.transCutoff:
36 --transCutoff $mode.transCutoff
37 #end if
38
39 #if $mode.sequencedCountCutoff:
40 --sequencedCountCutoff $mode.sequencedCountCutoff
41 #end if
42
43 $mode.skipDiagonal
44 $mode.perchr
45
46 #elif $mode.mode_selector == 'merge_failed':
47 --plotName diagnostic_plot.png
48 --outMatrixFile corrected_matrix.npz.h5
49 #if $mode.xMax:
50 --xMax $mode.xMax
51 #end if
52 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
53 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
54 #end if
55 #else:
56 --plotName diagnostic_plot.png
57 #if $mode.xMax:
58 --xMax $mode.xMax
59 #end if
60 #end if
61
62 ]]>
63 </command>
64 <inputs>
65 <param argument="--matrix" name="matrix" type="data" format="h5"
66 label="Hi-C matrix" />
67
68 <conditional name="mode">
69 <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
70 <option value="diagnostic_plot">Diagnostic plot</option>
71 <option value="correct">Correct matrix</option>
72 </param>
73 <when value="diagnostic_plot">
74 <expand macro="xMax" />
75 </when>
76 <when value="correct">
77 <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
78 label="Number of iterations" />
79
80 <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
81 label="Inflation cutoff" value=""
82 help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
83 For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/>
84
85 <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
86 label="Trans region cutoff" value=""
87 help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>
88
89 <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
90 label="Sequenced count cutoff"
91 help="Each bin receives a value indicating the fraction that is covered by reads.
92 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
93
94 <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
95 label="Skip diagonal counts"/>
96
97 <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
98 label="Normalize each chromosome separately" />
99 <expand macro="filterThreshold" />
100
101 </when>
102 </conditional>
103
104 <repeat name="chromosomes" min="1"
105 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
106 The order of the given chromosomes will be kept for the resulting corrected matrix">
107 <param name="chromosome" type="text" value="" />
108 </repeat>
109
110 </inputs>
111 <outputs>
112 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5">
113 <filter>mode['mode_selector'] == "correct"</filter>
114 </data>
115 <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
116 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
117 </data>
118 </outputs>
119 <tests>
120 <test>
121 <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
122 <param name="mode_selector" value="correct"/>
123 <repeat name="chromosomes">
124 <param name="chromosome" value="chrUextra"/>
125 </repeat>
126 <repeat name="chromosomes">
127 <param name="chromosome" value="chr3LHet"/>
128 </repeat>
129 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
130 </test>
131 <test>
132 <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/>
133 <param name="mode_selector" value="diagnostic_plot"/>
134 <repeat name="chromosomes">
135 <param name="chromosome" value="chrUextra"/>
136 </repeat>
137 <repeat name="chromosomes">
138 <param name="chromosome" value="chr3LHet"/>
139 </repeat>
140 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
141 </test>
142 </tests>
143 <help><![CDATA[
144
145 **What it does**
146
147 Runs Dekker's iterative correction over a hic matrix.
148
149
150 correct Run the iterative correction.
151 diagnostic_plot
152 Plots a histogram of the coverage per bin together with the
153 modified z-score based on the median absolute deviation
154 method (see Boris Iglewicz and David Hoaglin 1993, Volume
155 16: How to Detect and Handle Outliers The ASQC Basic
156 References in Quality Control: Statistical Techniques,
157 Edward F. Mykytka, Ph.D., Editor.
158
159
160 ]]></help>
161 <expand macro="citations" />
162 </tool>
163