Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 13:40b33e101621 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:45:27 -0500
parents 653c6fead9f9
children fe13295d0329
comparison
equal deleted inserted replaced
12:492c1c966a22 13:40b33e101621
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 16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
17 @BINARY@ 17 @BINARY@
18 18
19 --matrix '$matrix_h5_cooler' 19
20 --matrix 'matrix.$matrix_h5_cooler.ext'
20 21
21 #if $title and $title is not None: 22 #if $title and $title is not None:
22 --title '$title' 23 --title '$title'
23 #end if 24 #end if
24 25
30 31
31 $perChromosome 32 $perChromosome
32 $clearMaskedBins 33 $clearMaskedBins
33 34
34 ## special: --chromosomeOrder is optional, but if given needs at least one argument 35 ## special: --chromosomeOrder is optional, but if given needs at least one argument
35 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) 36 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
36 #if chroms: 37 #if chroms:
37 --chromosomeOrder "$chroms" 38 --chromosomeOrder "$chroms"
38 #end if 39 #end if
39 40
40 #if $region: 41 #if $region:
56 #end if 57 #end if
57 58
58 #if $vMax: 59 #if $vMax:
59 --vMax $vMax 60 --vMax $vMax
60 #end if 61 #end if
61 62
63 #if str($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
62 $pca 70 $pca
63 71 #if $dpi:
72 --dpi $dpi
73 #end if
74
75 #if $loops:
76 --loops '$loops'
77 #end if
64 && mv plot.$image_file_format plot 78 && mv plot.$image_file_format plot
65 ]]> 79 ]]>
66 </command> 80 </command>
67 <inputs> 81 <inputs>
68 <expand macro='matrix_h5_cooler_macro' /> 82 <expand macro='matrix_h5_cooler_macro' />
101 </param> 115 </param>
102 <when value='' /> 116 <when value='' />
103 <when value='bigwig'> 117 <when value='bigwig'>
104 <param name='pca_bigwig' type="data" format="bigwig" 118 <param name='pca_bigwig' type="data" format="bigwig"
105 label="Eigenvector file"/> 119 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
106 </when> 127 </when>
107 </conditional> 128 </conditional>
129 <param name='loops' type="data" format="interval" optional='True' label="Add detected loops"/>
108 <param name="image_file_format" type="select" label="Image output format"> 130 <param name="image_file_format" type="select" label="Image output format">
109 <option value="png" selected="True">png</option> 131 <option value="png" selected="True">png</option>
110 <option value="svg">svg</option> 132 <option value="svg">svg</option>
133 <option value="pdf">pdf</option>
134
111 </param> 135 </param>
136 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
112 </inputs> 137 </inputs>
113 <outputs> 138 <outputs>
114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> 139 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
115 <change_format> 140 <change_format>
116 <when input="image_file_format" value="svg" format="svg" /> 141 <when input="image_file_format" value="svg" format="svg" />
142 <when input="image_file_format" value="pdf" format="pdf" />
117 </change_format> 143 </change_format>
118 </data> 144 </data>
119 </outputs> 145 </outputs>
120 <tests> 146 <tests>
121 <test> 147 <test>
122 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> 148 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
123 <conditional name="pca_conditional"> 149 <conditional name="pca_conditional">
124 <param name="pca_type" value=''/> 150 <param name="pca_type" value=''/>
125 </conditional> 151 </conditional>
126 <param name="region" value="chrX:3000000-3500000"/> 152 <param name="region" value="chr2L:3000000-3500000"/>
127 <param name="region2" value="chrX:3100000-3600000"/> 153 <param name="region2" value="chr2L:3100000-3600000"/>
128 <param name="log1p" value="True"/> 154 <param name="log1p" value="True"/>
129 <param name="clearMaskedBins" value="True"/> 155 <param name="clearMaskedBins" value="True"/>
130 <param name="image_file_format" value="png" /> 156 <param name="image_file_format" value="png" />
131 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/> 157 <param name="dpi" value="10" />
158
159 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size"/>
132 </test> 160 </test>
133 <test> 161 <test>
134 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/> 162 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
163 <param name="region" value="chr2L:3000000-3500000"/>
164
135 <conditional name="pca_conditional"> 165 <conditional name="pca_conditional">
136 <param name="pca_type" value=''/> 166 <param name="pca_type" value=''/>
137 </conditional> 167 </conditional>
138 <param name="region" value="X:3000000-3500000"/> 168 <param name="image_file_format" value="pdf" />
139 <param name="image_file_format" value="png" /> 169 <param name="dpi" value="10" />
140 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/> 170
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"/>
145 <conditional name="pca_conditional"> 175 <conditional name="pca_conditional">
146 <param name="pca_type" value='bigwig'/> 176 <param name="pca_type" value='bigwig'/>
147 <param name="pca_bigwig" value="pca1.bw"/> 177 <param name="pca_bigwig" value="hicPCA/pca1_test1.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'/>
148 </conditional> 182 </conditional>
149 <param name='colormap' value='hot'/> 183 <param name='colormap' value='hot'/>
184 <param name="region" value="chr2L:3000000-3500000"/>
185 <param name="dpi" value="10" />
186
150 <param name="image_file_format" value="svg" /> 187 <param name="image_file_format" value="svg" />
151 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> 188 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/>
152 </test> 189 </test>
153 <test> 190
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>
165 </tests> 191 </tests>
166 <help><![CDATA[ 192 <help><![CDATA[
167 Contact matrix plot 193 Contact matrix plot
168 ======================= 194 =======================
169 195