Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison macros.xml @ 5:3bc1425f9000 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:26:27 -0500
parents 652fdcbff650
children 30d427846764
comparison
equal deleted inserted replaced
4:652fdcbff650 5:3bc1425f9000
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">1.8.1</token> 3 <token name="@WRAPPER_VERSION@">2.0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> 6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
7 <yield /> 7 <yield />
8 </requirements> 8 </requirements>
9 <version_command>@BINARY@ --version</version_command> 9 <version_command>@BINARY@ --version</version_command>
10 </xml> 10 </xml>
11 11
12 <xml name="citations"> 12 <xml name="citations">
13 <citations> 13 <citations>
14 <citation type="doi">10.5281/zenodo.159780</citation> 14 <citation type="doi">10.5281/zenodo.1123667</citation>
15 <yield /> 15 <yield />
16 </citations> 16 </citations>
17 </xml> 17 </xml>
18 18
19 <xml name="zMax"> 19 <xml name="zMax">
164 </xml> 164 </xml>
165 165
166 166
167 <xml name="multiple_input_matrices"> 167 <xml name="multiple_input_matrices">
168 <repeat name="input_files" title="HiC Matrix files" min="2"> 168 <repeat name="input_files" title="HiC Matrix files" min="2">
169 <param name="matrix" type="data" format="h5" 169 <param name="matrix" type="data" format="h5,cool"
170 label="HiC Matrix file" 170 label="HiC Matrix file"
171 help=""/> 171 help=""/>
172 <param name="mlabel" type="text" size="30" optional="true" value="" 172 <param name="mlabel" type="text" size="30" optional="true" value=""
173 label="Label" 173 label="Label"
174 help="Label to use in the output. If not given the dataset name will be used instead."/> 174 help="Label to use in the output. If not given the dataset name will be used instead."/>
177 177
178 <token name="@multiple_input_matrices@"> 178 <token name="@multiple_input_matrices@">
179 #set $matrices = [] 179 #set $matrices = []
180 #set $mlabels = [] 180 #set $mlabels = []
181 #for $counter, $i in enumerate($input_files): 181 #for $counter, $i in enumerate($input_files):
182 ln -s $i.matrix #echo str($counter)+'.npz.h5'#; 182 ln -s $i.matrix #echo str($counter)+'_matrix'#;
183 #silent $matrices.append( '%s.npz.h5' % $counter ) 183 #silent $matrices.append( '%s_matrix' % $counter )
184 184
185 #if str($i.mlabel.value) != "": 185 #if str($i.mlabel.value) != "":
186 #set $mlabels += ['"%s"' % ($i.mlabel.value)] 186 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
187 #else 187 #else
188 #set $mlabels += ['"%s"' % ($i.matrix.name)] 188 #set $mlabels += ['"%s"' % ($i.matrix.name)]
297 297
298 298
299 <xml name="pseudocount"> 299 <xml name="pseudocount">
300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> 300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
301 </xml> 301 </xml>
302 302 <xml name='matrix_h5_cooler_macro'>
303 <param name='matrix_h5_cooler' type="data" format="h5,cool"
304 label="Matrix to compute on."/>
305
306 </xml>
307 <xml name='matrix_h5_cooler_multiple_macro'>
308 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
309 label="Matrix to compute on." multiple="True"/>
310 </xml>
303 <token name="@REFERENCES@"> 311 <token name="@REFERENCES@">
304 312
305 .. class:: infomark 313 .. class:: infomark
306 314
307 For more information on the tools, please visit our `help site`_. 315 For more information on the tools, please visit our `help site`_.
523 </filter> 531 </filter>
524 </data> 532 </data>
525 </xml> 533 </xml>
526 534
527 <xml name="track_input_h5_macro"> 535 <xml name="track_input_h5_macro">
528 <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/> 536 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
529 </xml> 537 </xml>
530 <xml name="track_input_bed_macro"> 538 <xml name="track_input_bed_macro">
531 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> 539 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
532 </xml> 540 </xml>
533 <xml name="track_input_bedgraph_macro"> 541 <xml name="track_input_bedgraph_macro">