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comparison physiofit.xml @ 1:52dddad92226 draft

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planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 3d93a125fa9636cc64663a0e94f3e089eb2d8aff
author workflow4metabolomics
date Wed, 16 Nov 2022 17:16:06 +0000
parents 198d81ccc75e
children 232ad69fc93c
comparison
equal deleted inserted replaced
0:198d81ccc75e 1:52dddad92226
1 <tool id='physiofit' name='PhysioFit' profile='21.09' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5'> 1 <tool id='physiofit' name='PhysioFit' profile='21.09' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5'>
2 <description>Extracellular flux analysis</description> 2 <description>Extracellular flux analysis</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.1.0</token> 4 <token name="@TOOL_VERSION@">2.2.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type='package' version='@TOOL_VERSION@'>physiofit4galaxy</requirement> 7 <requirement type='package' version='@TOOL_VERSION@'>physiofit4galaxy</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors='exit_code'><![CDATA[ 9 <command detect_errors='exit_code'><![CDATA[
23 #if $basic_settings.lag: 23 #if $basic_settings.lag:
24 -l 24 -l
25 #end if 25 #end if
26 26
27 #if $basic_settings.deg_select.deg == 'Yes': 27 #if $basic_settings.deg_select.deg == 'Yes':
28 -d '$basic_setting.degconsts' 28 -d '$basic_settings.deg_select.degconsts'
29 #end if 29 #end if
30 30
31 #if $basic_settings.mc_select.montecarlo == 'Yes': 31 #if $basic_settings.mc_select.montecarlo == 'Yes':
32 -mc '$basic_settings.mc_select.iters' 32 -mc '$basic_settings.mc_select.iters'
33 #end if 33 #end if
56 56
57 #if $advanced_settings.verbose: 57 #if $advanced_settings.verbose:
58 -v 58 -v
59 #end if 59 #end if
60 60
61 -op '$plots' -of '$fluxes' -os '$stats' -oc '$config' 61 -op '$plots' -of '$fluxes' -os '$stats' -oc '$config' 2> $log
62 62
63 ]]></command> 63 ]]></command>
64 <inputs> 64 <inputs>
65 65
66 <conditional name='input_selection'> 66 <conditional name='input_selection'>
86 <param name='deg' type='select' label='Select yes to add degradation constants'> 86 <param name='deg' type='select' label='Select yes to add degradation constants'>
87 <option value='No'>No</option> 87 <option value='No'>No</option>
88 <option value='Yes'>Yes</option> 88 <option value='Yes'>Yes</option>
89 </param> 89 </param>
90 <when value='Yes'> 90 <when value='Yes'>
91 <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'/> 91 <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'>
92 <sanitizer>
93 <valid>
94 <add value='"'/>
95 <add value='{'/>
96 <add value='}'/>
97 </valid>
98 </sanitizer>
99 </param>
92 </when> 100 </when>
93 </conditional> 101 </conditional>
94 102
95 <conditional name='mc_select'> 103 <conditional name='mc_select'>
96 <param name='montecarlo' type='select' label='Select yes for sensitivity analysis'> 104 <param name='montecarlo' type='select' label='Select yes for sensitivity analysis'>
113 <param name='sd' type='select' label='Select yes to add standard deviations'> 121 <param name='sd' type='select' label='Select yes to add standard deviations'>
114 <option value='No'>No</option> 122 <option value='No'>No</option>
115 <option value='Yes'>Yes</option> 123 <option value='Yes'>Yes</option>
116 </param> 124 </param>
117 <when value='Yes'> 125 <when value='Yes'>
118 <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)' /> 126 <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)'>
127 <sanitizer>
128 <valid>
129 <add value='"'/>
130 <add value='{'/>
131 <add value='}'/>
132 </valid>
133 </sanitizer>
134 </param>
119 </when> 135 </when>
120 </conditional> 136 </conditional>
121 137
122 <conditional name='cm_select'> 138 <conditional name='cm_select'>
123 <param name='cm' type='select' label='Flag to add bounds on metabolite concentrations'> 139 <param name='cm' type='select' label='Flag to add bounds on metabolite concentrations'>
124 <option value='No'>No</option> 140 <option value='No'>No</option>
125 <option value='Yes'>Yes</option> 141 <option value='Yes'>Yes</option>
126 </param> 142 </param>
127 <when value='Yes'> 143 <when value='Yes'>
128 <param name='conc_met_bounds' type='text' value='()' label='Bounds on metabolite concentrations. Bounds should be given in tuple format (see docs for more information)' /> 144 <param name='conc_met_bounds' type='text' value='()' label='Bounds on metabolite concentrations. Bounds should be given in tuple format (see docs for more information)'/>
145
129 </when> 146 </when>
130 </conditional> 147 </conditional>
131 148
132 <conditional name='fm_select'> 149 <conditional name='fm_select'>
133 <param name='fm' type='select' label='Select yes to add bounds on metabolite fluxes'> 150 <param name='fm' type='select' label='Select yes to add bounds on metabolite fluxes'>
168 <outputs> 185 <outputs>
169 <data name='plots' label='Plots' format='pdf'/> 186 <data name='plots' label='Plots' format='pdf'/>
170 <data name='fluxes' label='Flux_results' format='tabular'/> 187 <data name='fluxes' label='Flux_results' format='tabular'/>
171 <data name='stats' label='Stat_results' format='tabular'/> 188 <data name='stats' label='Stat_results' format='tabular'/>
172 <data name='config' label='Config_file' format='json'/> 189 <data name='config' label='Config_file' format='json'/>
190 <data name='log' label='Run_Log' format='txt'/>
173 </outputs> 191 </outputs>
174 192
175 <tests> 193 <tests>
176 <test> 194 <test>
177 <param name='input_selection|input_selector' value='tsv' /> 195 <param name='input_selection|input_selector' value='tsv' />
196 <has_n_lines n='7'/> 214 <has_n_lines n='7'/>
197 <has_size value='767' delta='20'/> 215 <has_size value='767' delta='20'/>
198 </assert_contents> 216 </assert_contents>
199 </output> 217 </output>
200 </test> 218 </test>
219 <!-- <test>-->
220 <!-- <param name='input_selection|input_selector' value='tsv' />-->
221 <!-- <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />-->
222 <!-- <section name='basic_settings'>-->
223 <!-- <param name='lag' value='No'/>-->
224 <!-- <param name='deg_select|deg' value='No'/>-->
225 <!-- <param name='mc_select|montecarlo' value='No'/>-->
226 <!-- </section>-->
227 <!-- <section name='advanced_settings'>-->
228 <!-- <param name='vini' value='1'/>-->
229 <!-- <param name='sd_select|sd' value='No'/>-->
230 <!-- <param name='cm_select|cm' value='No'/>-->
231 <!-- <param name='fm_select|fm' value='No'/>-->
232 <!-- <param name='cb_select|cb' value='No'/>-->
233 <!-- <param name='fb_select|fb' value='No'/>-->
234 <!-- <param name='verbose' value='No'/>-->
235 <!-- </section>-->
236 <!-- <output name='fluxes' file='flux_results.tsv'/>-->
237 <!-- </test>-->
201 </tests> 238 </tests>
202 239
203 <help><![CDATA[ 240 <help><![CDATA[
204 .. class:: warningmark 241 .. class:: warningmark
205 242