# HG changeset patch
# User workflow4metabolomics
# Date 1668618966 0
# Node ID 52dddad92226f115f3e0ae8cee8bcfe6b8ba3dcd
# Parent  198d81ccc75e1ff32f8898e30fab03cb7ed33ce8
planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 3d93a125fa9636cc64663a0e94f3e089eb2d8aff

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[
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
@@ -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