Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 8:d398f5373c70 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:44:12 -0500
parents f93a78bc045e
children 653c6fead9f9
comparison
equal deleted inserted replaced
7:f93a78bc045e 8:d398f5373c70
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 9
10 #if str($pca_conditional.pca_type) == 'bedgraph': 10 #if str($pca_conditional.pca_type) == 'bigwig':
11 ln -s $pca_conditional.pca_bedgraph pca.bedgraph &&
12 #set $pca = '--pca pca.bedgraph'
13 #elif str($pca_conditional.pca_type) == 'bigwig':
14 ln -s $pca_conditional.pca_bigwig pca.bw && 11 ln -s $pca_conditional.pca_bigwig pca.bw &&
15 #set $pca = '--pca pca.bw' 12 #set $pca = '--bigwig pca.bw'
16 #elif str($pca_conditional.pca_type) == '': 13 #elif str($pca_conditional.pca_type) == '':
17 #set $pca = '' 14 #set $pca = ''
18 #end if 15 #end if
19 16
20 @BINARY@ 17 @BINARY@
98 <param argument="--vMax" type="float" optional="true" label="vMax"/> 95 <param argument="--vMax" type="float" optional="true" label="vMax"/>
99 96
100 <conditional name="pca_conditional"> 97 <conditional name="pca_conditional">
101 <param name='pca_type' label='Datatype of eigenvector file' type='select'> 98 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
102 <option value='' selected="true"></option> 99 <option value='' selected="true"></option>
103 <option value='bedgraph'>bedgraph</option>
104 <option value='bigwig'>bigwig</option> 100 <option value='bigwig'>bigwig</option>
105 </param> 101 </param>
106 <when value='' /> 102 <when value='' />
107 <when value='bedgraph'>
108 <param name='pca_bedgraph' type="data" format="bedgraph"
109 label="Eigenvector file"/>
110 </when>
111 <when value='bigwig'> 103 <when value='bigwig'>
112 <param name='pca_bigwig' type="data" format="bigwig" 104 <param name='pca_bigwig' type="data" format="bigwig"
113 label="Eigenvector file"/> 105 label="Eigenvector file"/>
114 </when> 106 </when>
115 </conditional> 107 </conditional>
149 </test> 141 </test>
150 <test> 142 <test>
151 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/> 143 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
152 <param name="perChromosome" value="True"/> 144 <param name="perChromosome" value="True"/>
153 <conditional name="pca_conditional"> 145 <conditional name="pca_conditional">
154 <param name="pca_type" value='bedgraph'/> 146 <param name="pca_type" value='bigwig'/>
155 <param name="pca_bedgraph" value="pca1.bedgraph"/> 147 <param name="pca_bigwig" value="pca1.bw"/>
156 </conditional> 148 </conditional>
157 <param name='colormap' value='hot'/> 149 <param name='colormap' value='hot'/>
158 <param name="image_file_format" value="svg" /> 150 <param name="image_file_format" value="svg" />
159 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> 151 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
160 </test> 152 </test>
191 - What to show: 183 - What to show:
192 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used. 184 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
193 - log / log1p of the values: It is recommended to use log1p. 185 - log / log1p of the values: It is recommended to use log1p.
194 - Colormaps_ for the heatmap. 186 - Colormaps_ for the heatmap.
195 - vMin / vMax 187 - vMin / vMax
196 - principal component: a bedgraph or bigwig file containing eigenvector information 188 - principal component: a bigwig file containing eigenvector information
197 189
198 Output 190 Output
199 ------ 191 ------
200 192
201 The contact matrix plotted for chromosome 1. 193 The contact matrix plotted for chromosome 1.