comparison hicAggregateContacts.xml @ 13:f0216498a666 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:18:29 +0000
parents e30485c5e93b
children
comparison
equal deleted inserted replaced
12:e30485c5e93b 13:f0216498a666
64 #end if 64 #end if
65 65
66 #if $vMax: 66 #if $vMax:
67 --vMax $vMax 67 --vMax $vMax
68 #end if 68 #end if
69 69
70 $considerStrandDirection
71
70 --outFileName plot.$image_file_format 72 --outFileName plot.$image_file_format
71 && 73 &&
72 mv plot.$image_file_format plot 74 mv plot.$image_file_format plot
73 #if $outputs and 'outFileObsExp' in $outputs: 75 #if $outputs and 'outFileObsExp' in $outputs:
74 && mv 'ObsExp.$matrix_h5_cooler.ext' matrix 76 && mv 'ObsExp.$matrix_h5_cooler.ext' matrix
75 #end if 77 #end if
76 78
77 ]]> 79 ]]>
78 </command> 80 </command>
79 <inputs> 81 <inputs>
80 <expand macro='matrix_h5_cooler_macro' /> 82 <expand macro="matrix_h5_cooler_macro" />
81 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" /> 83 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
82 <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" /> 84 <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />
83 85
84 <expand macro='range' /> 86 <expand macro="range" />
85 <param argument="--mode" type="select" label="Regions to consider."> 87 <param argument="--mode" type="select" label="Regions to consider.">
86 <option value="inter-chr">inter-chr</option> 88 <option value="inter-chr">inter-chr</option>
87 <option value="intra-chr">intra-chr</option> 89 <option value="intra-chr">intra-chr</option>
88 <option value="all" selected="true">all</option> 90 <option value="all" selected="true">all</option>
89 </param> 91 </param>
117 <param argument="--operationType" type="select" label="Type of operation to compute final matrix"> 119 <param argument="--operationType" type="select" label="Type of operation to compute final matrix">
118 <option value="median" selected="true">median</option> 120 <option value="median" selected="true">median</option>
119 <option value="mean">mean</option> 121 <option value="mean">mean</option>
120 <option value="sum">sum</option> 122 <option value="sum">sum</option>
121 </param> 123 </param>
124 <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />
122 125
123 <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 126 <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than
124 a bin of the input matrix, by default only the first bin 127 a bin of the input matrix, by default only the first bin
125 is taken into account. However there are more posibilities 128 is taken into account. However there are more posibilities
126 to handel such a case. Users can ask for the last bin or 129 to handel such a case. Users can ask for the last bin or
187 </collection> 190 </collection>
188 <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Heatmap"> 191 <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Heatmap">
189 <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" /> 192 <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
190 </collection> 193 </collection>
191 <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> 194 <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
192 <filter>'outFileObsExp' in outputs</filter> 195 <filter>outputs == 'outFileObsExp'</filter>
193 <change_format> 196 <change_format>
194 <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> 197 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
195 </change_format> 198 </change_format>
196 </data> 199 </data>
197 </outputs> 200 </outputs>
198 <tests> 201 <tests>
199 <test> 202 <test expect_num_outputs="4">
200 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" /> 203 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
201 <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" /> 204 <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
202 <param name="numberOfBins" value="30" /> 205 <param name="numberOfBins" value="30" />
203 <param name="range_max" value="900000" /> 206 <param name="range_max" value="900000" />
204 <param name="range_min" value="50000" /> 207 <param name="range_min" value="50000" />