| Previous changeset 0:198d81ccc75e (2022-10-28) Next changeset 2:232ad69fc93c (2024-01-16) |
|
Commit message:
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 3d93a125fa9636cc64663a0e94f3e089eb2d8aff |
|
modified:
physiofit.xml test-data/flux_results.tsv |
| b |
| diff -r 198d81ccc75e -r 52dddad92226 physiofit.xml --- a/physiofit.xml Fri Oct 28 10:25:15 2022 +0000 +++ b/physiofit.xml Wed Nov 16 17:16:06 2022 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <tool id='physiofit' name='PhysioFit' profile='21.09' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5'> <description>Extracellular flux analysis</description> <macros> - <token name="@TOOL_VERSION@">2.1.0</token> + <token name="@TOOL_VERSION@">2.2.1</token> </macros> <requirements> <requirement type='package' version='@TOOL_VERSION@'>physiofit4galaxy</requirement> @@ -25,7 +25,7 @@ #end if #if $basic_settings.deg_select.deg == 'Yes': - -d '$basic_setting.degconsts' + -d '$basic_settings.deg_select.degconsts' #end if #if $basic_settings.mc_select.montecarlo == 'Yes': @@ -58,7 +58,7 @@ -v #end if - -op '$plots' -of '$fluxes' -os '$stats' -oc '$config' + -op '$plots' -of '$fluxes' -os '$stats' -oc '$config' 2> $log ]]></command> <inputs> @@ -88,7 +88,15 @@ <option value='Yes'>Yes</option> </param> <when value='Yes'> - <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'/> + <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'> + <sanitizer> + <valid> + <add value='"'/> + <add value='{'/> + <add value='}'/> + </valid> + </sanitizer> + </param> </when> </conditional> @@ -115,7 +123,15 @@ <option value='Yes'>Yes</option> </param> <when value='Yes'> - <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)' /> + <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)'> + <sanitizer> + <valid> + <add value='"'/> + <add value='{'/> + <add value='}'/> + </valid> + </sanitizer> + </param> </when> </conditional> @@ -125,7 +141,8 @@ <option value='Yes'>Yes</option> </param> <when value='Yes'> - <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)' /> + <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)'/> + </when> </conditional> @@ -170,6 +187,7 @@ <data name='fluxes' label='Flux_results' format='tabular'/> <data name='stats' label='Stat_results' format='tabular'/> <data name='config' label='Config_file' format='json'/> + <data name='log' label='Run_Log' format='txt'/> </outputs> <tests> @@ -198,6 +216,25 @@ </assert_contents> </output> </test> +<!-- <test>--> +<!-- <param name='input_selection|input_selector' value='tsv' />--> +<!-- <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />--> +<!-- <section name='basic_settings'>--> +<!-- <param name='lag' value='No'/>--> +<!-- <param name='deg_select|deg' value='No'/>--> +<!-- <param name='mc_select|montecarlo' value='No'/>--> +<!-- </section>--> +<!-- <section name='advanced_settings'>--> +<!-- <param name='vini' value='1'/>--> +<!-- <param name='sd_select|sd' value='No'/>--> +<!-- <param name='cm_select|cm' value='No'/>--> +<!-- <param name='fm_select|fm' value='No'/>--> +<!-- <param name='cb_select|cb' value='No'/>--> +<!-- <param name='fb_select|fb' value='No'/>--> +<!-- <param name='verbose' value='No'/>--> +<!-- </section>--> +<!-- <output name='fluxes' file='flux_results.tsv'/>--> +<!-- </test>--> </tests> <help><![CDATA[ |
| b |
| diff -r 198d81ccc75e -r 52dddad92226 test-data/flux_results.tsv --- a/test-data/flux_results.tsv Fri Oct 28 10:25:15 2022 +0000 +++ b/test-data/flux_results.tsv Wed Nov 16 17:16:06 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ optimal mean sd median CI_2.5 CI_97.5 -X_0 0.019837910042084236 0.020055047719088507 0.001936242015519126 0.020181433524903817 0.016385933648857588 0.023991705722000656 -mu 0.6448503161617235 0.6442401851491355 0.019838552319737378 0.6422759597671867 0.6055123753172559 0.6830180317435467 -Glc_q -6.7962941185743135 -6.774793454329362 0.39318776265927613 -6.801632529773193 -7.486259488979566 -6.0294828984301505 -Glc_M0 13.890941548678349 13.881503136428412 0.2268604387133866 13.89390411710686 13.42167220505119 14.364675598831429 -Ace_q 2.574083305172119 2.5516892907444007 0.34218910204223774 2.5706434692350855 1.8525815217489552 3.109731754802952 -Ace_M0 0.28632420734796105 0.28673563941751923 0.17207412150016024 0.2778487391600317 1e-06 0.6251737133158014 +X_0 0.030057356085279038 0.031020693652716442 0.01248214419475165 0.029507198033154346 0.011641988888053973 0.058342137145944405 +mu 0.5582759125316301 0.5686092117011008 0.08528431418544957 0.5617732771700231 0.4274326438805963 0.7428252946602405 +Glc_q -6.4690012286708845 -6.591939336986598 0.9573465913461194 -6.424216065589273 -8.689007040053548 -5.0804721629347975 +Glc_M0 14.102913181701245 14.093239782222746 0.3546457036884282 14.067487732809713 13.440594995883767 14.729084422532983 +Ace_q 2.4965870596545154 2.476648498253909 0.498894590813266 2.4157877116089033 1.7499997734065047 3.472079451670515 +Ace_M0 0.17844344816654867 0.20546717227239447 0.1953912180223188 0.17549120518463776 1e-06 0.7122213079215097 |