Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 16:96c472622ebc draft

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"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author bgruening
date Mon, 16 Dec 2019 13:20:28 +0000
parents 4053214bebac
children 83bda473a3f7
comparison
equal deleted inserted replaced
15:4053214bebac 16:96c472622ebc
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($pca_conditional.pca_type) == 'bigwig': 10 #if str($pca_conditional.pca_type) == 'bigwig':
11 ln -s '$pca_conditional.pca_bigwig' pca.bw && 11 ln -s $pca_conditional.pca_bigwig pca.bw &&
12 #set $pca = '--bigwig pca.bw' 12 #set $pca = '--bigwig pca.bw'
13 #elif str($pca_conditional.pca_type) == '': 13 #elif str($pca_conditional.pca_type) == '':
14 #set $pca = '' 14 #set $pca = ''
15 #end if 15 #end if
16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext && 16
17 @BINARY@ 17 @BINARY@
18 18
19 19 --matrix '$matrix_h5_cooler'
20 --matrix 'matrix.$matrix_h5_cooler.ext'
21 20
22 #if $title and $title is not None: 21 #if $title and $title is not None:
23 --title '$title' 22 --title '$title'
24 #end if 23 #end if
25 24
31 30
32 $perChromosome 31 $perChromosome
33 $clearMaskedBins 32 $clearMaskedBins
34 33
35 ## special: --chromosomeOrder is optional, but if given needs at least one argument 34 ## special: --chromosomeOrder is optional, but if given needs at least one argument
36 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ]) 35 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
37 #if chroms: 36 #if chroms:
38 --chromosomeOrder "$chroms" 37 --chromosomeOrder "$chroms"
39 #end if 38 #end if
40 39
41 #if $region: 40 #if $region:
57 #end if 56 #end if
58 57
59 #if $vMax: 58 #if $vMax:
60 --vMax $vMax 59 --vMax $vMax
61 #end if 60 #end if
62 61
63 #if str($pca_conditional.pca_type) == 'bigwig':
64 --vMinBigwig $pca_conditional.vMinBigwig
65 --vMaxBigwig $pca_conditional.vMaxBigwig
66 $pca_conditional.flipBigwigSign
67 --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
68 $pca_conditional.bigwigAdditionalVerticalAxis
69 #end if
70 $pca 62 $pca
71 #if $dpi: 63
72 --dpi $dpi
73 #end if
74
75 #if $loops:
76 --loops '$loops'
77 #end if
78 && mv plot.$image_file_format plot 64 && mv plot.$image_file_format plot
79 ]]> 65 ]]>
80 </command> 66 </command>
81 <inputs> 67 <inputs>
82 <expand macro='matrix_h5_cooler_macro' /> 68 <expand macro='matrix_h5_cooler_macro' />
115 </param> 101 </param>
116 <when value='' /> 102 <when value='' />
117 <when value='bigwig'> 103 <when value='bigwig'>
118 <param name='pca_bigwig' type="data" format="bigwig" 104 <param name='pca_bigwig' type="data" format="bigwig"
119 label="Eigenvector file"/> 105 label="Eigenvector file"/>
120 <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score."/>
121 <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score."/>
122 <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' />
123 <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor."/>
124 <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' />
125
126
127 </when> 106 </when>
128 </conditional> 107 </conditional>
129 <param name='loops' type="data" format="interval" optional='True' label="Add detected loops"/>
130 <param name="image_file_format" type="select" label="Image output format"> 108 <param name="image_file_format" type="select" label="Image output format">
131 <option value="png" selected="True">png</option> 109 <option value="png" selected="True">png</option>
132 <option value="svg">svg</option> 110 <option value="svg">svg</option>
133 <option value="pdf">pdf</option>
134
135 </param> 111 </param>
136 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
137 </inputs> 112 </inputs>
138 <outputs> 113 <outputs>
139 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> 114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
140 <change_format> 115 <change_format>
141 <when input="image_file_format" value="svg" format="svg" /> 116 <when input="image_file_format" value="svg" format="svg" />
142 <when input="image_file_format" value="pdf" format="pdf" />
143 </change_format> 117 </change_format>
144 </data> 118 </data>
145 </outputs> 119 </outputs>
146 <tests> 120 <tests>
147 <test> 121 <test>
148 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 122 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
149 <conditional name="pca_conditional"> 123 <conditional name="pca_conditional">
150 <param name="pca_type" value=''/> 124 <param name="pca_type" value=''/>
151 </conditional> 125 </conditional>
152 <param name="region" value="chr2L:3000000-3500000"/> 126 <param name="region" value="chrX:3000000-3500000"/>
153 <param name="region2" value="chr2L:3100000-3600000"/> 127 <param name="region2" value="chrX:3100000-3600000"/>
154 <param name="log1p" value="True"/> 128 <param name="log1p" value="True"/>
155 <param name="clearMaskedBins" value="True"/> 129 <param name="clearMaskedBins" value="True"/>
156 <param name="image_file_format" value="png" /> 130 <param name="image_file_format" value="png" />
157 <param name="dpi" value="10" /> 131 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
158 132 </test>
159 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size"/> 133 <test>
160 </test> 134 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/>
161 <test>
162 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
163 <param name="region" value="chr2L:3000000-3500000"/>
164
165 <conditional name="pca_conditional"> 135 <conditional name="pca_conditional">
166 <param name="pca_type" value=''/> 136 <param name="pca_type" value=''/>
167 </conditional> 137 </conditional>
168 <param name="image_file_format" value="pdf" /> 138 <param name="region" value="X:3000000-3500000"/>
169 <param name="dpi" value="10" /> 139 <param name="image_file_format" value="png" />
170 140 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/>
171 <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size"/> 141 </test>
172 </test> 142 <test>
173 <test> 143 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
174 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 144 <param name="perChromosome" value="True"/>
175 <conditional name="pca_conditional"> 145 <conditional name="pca_conditional">
176 <param name="pca_type" value='bigwig'/> 146 <param name="pca_type" value='bigwig'/>
177 <param name="pca_bigwig" value="hicPCA/pca1_test1.bw"/> 147 <param name="pca_bigwig" value="pca1.bw"/>
178 <param name='vMinBigwig' value='10'/>
179 <param name='vMaxBigwig' value='20'/>
180 <param name='scaleFactorBigwig' value='2000'/>
181 <param name='flipBigwigSign' value='True'/>
182 </conditional> 148 </conditional>
183 <param name='colormap' value='hot'/> 149 <param name='colormap' value='hot'/>
184 <param name="region" value="chr2L:3000000-3500000"/>
185 <param name="dpi" value="10" />
186
187 <param name="image_file_format" value="svg" /> 150 <param name="image_file_format" value="svg" />
188 <output name="outFileName" file="hicPlotMatrix/plot3_pca.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'/>
189 </test> 152 </test>
190 153 <test>
154 <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/>
155 <param name="perChromosome" value="True"/>
156 <conditional name="pca_conditional">
157 <param name="pca_type" value='bigwig'/>
158 <param name="pca_bigwig" value="pca1.bw"/>
159 </conditional>
160 <param name='colormap' value='hot'/>
161
162 <param name="image_file_format" value="svg" />
163 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
164 </test>
191 </tests> 165 </tests>
192 <help><![CDATA[ 166 <help><![CDATA[
193 Contact matrix plot 167 Contact matrix plot
194 ======================= 168 =======================
195 169