Mercurial > repos > bimib > cobraxy

changeset 536:55fdc97cd95a draft

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Uploaded
author francesco_lapi
date Sat, 25 Oct 2025 11:02:15 +0000
parents 3266da9d0404
children f79250e824b5
files COBRAxy/metabolicModel2Tabular.xml
diffstat 1 files changed, 23 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/metabolicModel2Tabular.xml	Sat Oct 25 10:57:10 2025 +0000
+++ b/COBRAxy/metabolicModel2Tabular.xml	Sat Oct 25 11:02:15 2025 +0000
@@ -17,17 +17,20 @@
         --tool_dir $__tool_directory__
         --medium_selector $cond_model.cond_medium.medium_selector
         #if $cond_model.model_selector == 'Custom_model'
-            --input $cond_model.input
-            --name $cond_model.input.element_identifier
+            --input "$cond_model.input"
+            --name "$cond_model.input.element_identifier"
+            --out_tabular "$out_tabular_custom"
+        #elif $cond_model.model_selector == 'ENGRO2'
+            --model "$cond_model.model_selector"
+            --name "$cond_model.model_selector"
+            --out_tabular "$out_tabular_engro2"
         #else
-            --model $cond_model.model_selector
-            --name $cond_model.model_selector
+            --model "$cond_model.model_selector"
+            --name "$cond_model.model_selector"
+            --out_tabular "$out_tabular_recon"
         #end if
-
-        --gene_format $cond_model.gene_format
-        
-        --out_log $log
-        --out_tabular $out_tabular
+        --gene_format "$cond_model.gene_format"
+        --out_log "$log"
         ]]>
     </command>
     <inputs>
@@ -93,13 +96,18 @@
 
     <outputs>
         <data name="log" format="txt" label="MetabolicModelSetting - Log" />
-        <data name="out_tabular" format="tabular" 
-              label="#if $cond_model.model_selector == 'Custom_model'
-                        ${cond_model.input.element_identifier}_model_tabular
-                    #else
-                        ${cond_model.model_selector}_model_tabular
-                    #end if"/>
+        
+        <data name="out_tabular_engro2" format="tabular" label="ENGRO2_model_tabular">
+            <filter>cond_model['model_selector'] == 'ENGRO2'</filter>
+        </data>
+        
+        <data name="out_tabular_recon" format="tabular" label="Recon_model_tabular">
+            <filter>cond_model['model_selector'] == 'Recon'</filter>
+        </data>
 
+        <data name="out_tabular_custom" format="tabular" label="Custom_model_tabular">
+            <filter>cond_model['model_selector'] == 'Custom_model'</filter>
+        </data>
     </outputs>
 
     <help>