Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 2:ecf11dda45f7 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:10:27 -0400
parents d5bf8c60d661
children b55d7936cbe0
comparison
equal deleted inserted replaced
1:1e0d8c6b3483 2:ecf11dda45f7
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 9
10 ln -s '$matrix' temp_matrix.npz.h5 && 10 ln -s '$matrix' temp_matrix.npz.h5 &&
11 11
12 hicCorrectMatrix 12 hicCorrectMatrix
13 $mode.mode_selector 13 $mode.mode_selector
14 --matrix temp_matrix.npz.h5 14 --matrix temp_matrix.npz.h5
48 --outMatrixFile corrected_matrix.npz.h5 48 --outMatrixFile corrected_matrix.npz.h5
49 #if $mode.xMax: 49 #if $mode.xMax:
50 --xMax $mode.xMax 50 --xMax $mode.xMax
51 #end if 51 #end if
52 #if $mode.filterThreshold_low and $mode.filterThreshold_large: 52 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
53 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large 53 --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large'
54 #end if 54 #end if
55 #else: 55 #else:
56 --plotName diagnostic_plot.png 56 --plotName diagnostic_plot.png
57 #if $mode.xMax: 57 #if $mode.xMax:
58 --xMax $mode.xMax 58 --xMax $mode.xMax
99 <expand macro="filterThreshold" /> 99 <expand macro="filterThreshold" />
100 100
101 </when> 101 </when>
102 </conditional> 102 </conditional>
103 103
104 <repeat name="chromosomes" min="1" 104 <repeat name="chromosomes" min="0"
105 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction. 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"> 106 The order of the given chromosomes will be kept for the resulting corrected matrix">
107 <param name="chromosome" type="text" value="" /> 107 <param name="chromosome" type="text" value="" >
108 <validator type="empty_field" />
109 </param>
108 </repeat> 110 </repeat>
109 111
110 </inputs> 112 </inputs>
111 <outputs> 113 <outputs>
112 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5"> 114 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5">
116 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> 118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
117 </data> 119 </data>
118 </outputs> 120 </outputs>
119 <tests> 121 <tests>
120 <test> 122 <test>
121 <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/> 123 <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
122 <param name="mode_selector" value="correct"/> 124 <param name="mode_selector" value="correct"/>
123 <repeat name="chromosomes"> 125 <repeat name="chromosomes">
124 <param name="chromosome" value="chrUextra"/> 126 <param name="chromosome" value="chrUextra"/>
125 </repeat> 127 </repeat>
126 <repeat name="chromosomes"> 128 <repeat name="chromosomes">
127 <param name="chromosome" value="chr3LHet"/> 129 <param name="chromosome" value="chr3LHet"/>
128 </repeat> 130 </repeat>
129 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> 131 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
130 </test> 132 </test>
131 <test> 133 <test>
132 <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/> 134 <param name="matrix" ftype="h5" value="small_test_matrix.h5"/>
133 <param name="mode_selector" value="diagnostic_plot"/> 135 <param name="mode_selector" value="diagnostic_plot"/>
134 <repeat name="chromosomes"> 136 <repeat name="chromosomes">
135 <param name="chromosome" value="chrUextra"/> 137 <param name="chromosome" value="chrUextra"/>
136 </repeat> 138 </repeat>
137 <repeat name="chromosomes"> 139 <repeat name="chromosomes">
142 </tests> 144 </tests>
143 <help><![CDATA[ 145 <help><![CDATA[
144 146
145 **What it does** 147 **What it does**
146 148
147 Runs Dekker's iterative correction over a hic matrix. 149 Runs Dekker's iterative correction over a Hi-C matrix.
148 150
151 correct: Run the iterative correction.
149 152
150 correct Run the iterative correction. 153 diagnostic_plot: Plots a histogram of the coverage per bin together with the
151 diagnostic_plot 154 modified z-score based on the median absolute deviation
152 Plots a histogram of the coverage per bin together with the 155 method (see Boris Iglewicz and David Hoaglin 1993, Volume
153 modified z-score based on the median absolute deviation 156 16: How to Detect and Handle Outliers The ASQC Basic
154 method (see Boris Iglewicz and David Hoaglin 1993, Volume 157 References in Quality Control: Statistical Techniques,
155 16: How to Detect and Handle Outliers The ASQC Basic 158 Edward F. Mykytka, Ph.D., Editor.
156 References in Quality Control: Statistical Techniques,
157 Edward F. Mykytka, Ph.D., Editor.
158
159 159
160 ]]></help> 160 ]]></help>
161 <expand macro="citations" /> 161 <expand macro="citations" />
162 </tool> 162 </tool>
163 163