Mercurial > repos > bgruening > hicexplorer_hicconvertformat

comparison hicConvertFormat.xml @ 7:2a24ce221cd7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
author iuc
date Tue, 10 Jan 2023 19:02:29 +0000
parents 3e598b8e72e7
children c0737631eea1
comparison
equal deleted inserted replaced
6:3e598b8e72e7 7:2a24ce221cd7
86 @SINGLE_INPUT@ 86 @SINGLE_INPUT@
87 87
88 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector 88 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
89 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' 89 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
90 90
91 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
92 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
93 #else:
94 && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
95 #end if
96 #end if
97
98
99 ### Set up links to matrices to have correct ending 91 ### Set up links to matrices to have correct ending
100 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': 92 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
101 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': 93 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
102 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional 94 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
103 #if $xml_path.inputFormat_selector == 'optionCool': 95 #if $xml_path.inputFormat_selector == 'optionCool':
104 ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" && 96 ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" &&
105 #end if 97 #end if
204 #end if 196 #end if
205 197
206 --matrices $m 198 --matrices $m
207 #end if 199 #end if
208 --outFileName matrix.mcool 200 --outFileName matrix.mcool
201 #end if
202 $storeAppliedCorrection
203 $enforceInteger
204
205 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
206 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
207 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
208 #else:
209 && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
210 #end if
211 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
209 && mv matrix.mcool matrix_out 212 && mv matrix.mcool matrix_out
210 #end if 213 #end if
211 ]]> 214 ]]>
212 </command> 215 </command>
213 <inputs> 216 <inputs>
235 </when> 238 </when>
236 <when value='manyToOne_option'> 239 <when value='manyToOne_option'>
237 <expand macro='convertFormat_multiple_macro' /> 240 <expand macro='convertFormat_multiple_macro' />
238 </when> 241 </when>
239 </conditional> 242 </conditional>
240 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
241 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
242 </when> 243 </when>
243 </conditional> 244 </conditional>
245 <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" />
246 <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" />
244 </inputs> 247 </inputs>
245 <outputs> 248 <outputs>
246 <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'> 249 <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
247 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter> 250 <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter>
248 <change_format> 251 <change_format>