diff rpfba.xml @ 4:f297590100c8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 387d0dd233c1d9948152a2d4af9e69ad10fe1b6a

--- a/rpfba.xml	Thu Nov 02 14:35:58 2023 +0000
+++ b/rpfba.xml	Thu Nov 23 14:26:35 2023 +0000
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
         python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba'
             #if str($adv.merge) == "true":
-                --merge
+                --merge '$output_merge'
             #end if
                 --objective_rxn_id '$objective_rxn_id'
                 --sim '$input_sim_type.sim_type'
@@ -60,9 +60,12 @@
     </inputs>
     <outputs>
         <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
+        <data name="output_merge" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name} - merge">
+            <filter>adv['merge']</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
         <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  -->
             <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
@@ -74,11 +77,11 @@
                     <has_text text="5.54302" />
                     <!--check fba_biomass value-->
                     <has_text text="1.31359" />
-                    <has_n_lines n="396" />
+                    <has_n_lines n="455" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
         <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  and sim_type=fba-->
             <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
@@ -92,11 +95,11 @@
                     <!--check fba_fba value-->
                     <has_text text="16.47058" />
                     <not_has_text text="fba_fraction" />
-                    <has_n_lines n="380" />
+                    <has_n_lines n="415" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
         <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718)  and sim_type=pfba-->
             <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
@@ -110,7 +113,7 @@
                     <!--check fba_pfba value-->
                     <has_text text="2623.54248" />
                     <not_has_text text="fba_fraction" />
-                    <has_n_lines n="380" />
+                    <has_n_lines n="415" />
                 </assert_contents>
             </output>
         </test>