Update rptools

.github/workflows/pr.yaml

@@ -178,7 +178,9 @@ jobs:
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
     - name: Test
-      run: echo 'Repository list: ${{ needs.setup.outputs.repository-list }}'
+      run: |
+        echo "Repository list:"
+        echo "${{ needs.setup.outputs.repository-list }}"
     - uses: actions/upload-artifact@v3
       if: ${{ failure() }}
       with:

tools/rptools/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.3.2</token>
+    <token name="@TOOL_VERSION@">6.4.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>

tools/rptools/rpcompletion.xml

@@ -22,7 +22,7 @@
     ]]></command>
     <inputs>
         <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
-        <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
+        <param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" />
         <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
         <param name="sink" type="data" format="csv" label="Sink from SBML" />
         <section name="adv" title="Advanced Options" expanded="false">

tools/rptools/rpfba.xml

@@ -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>

tools/rptools/rpthermo.xml

@@ -43,7 +43,7 @@
                     <has_text text="-2308.11630" />
                     <!--check thermo_dG value-->
                     <has_text text="-2151.84763" />
-                    <has_n_lines n="473" />
+                    <has_n_lines n="522" />
                 </assert_contents>
             </output>
         </test>

tools/rptools/test-data/3-rp2paths_compounds.tsv

@@ -1,8 +1,33 @@
 Compound ID	Structure
-CMPD_0000000001	[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
-CMPD_0000000003	[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
-MNXM100	[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
-MNXM132	[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
-MNXM34	[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]
-MNXM83	[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]
-TARGET_0000000001	[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]
+CMPD_0000000003	[H]Oc1c([H])c([H])c([H])c([H])c1O[H]
+CMPD_0000000005	[H]c1c([H])c([H])c(N([H])[H])c([H])c1[H]
+CMPD_0000000007	[H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H]
+CMPD_0000000008	[H]OC(=O)c1c([H])c([H])c([H])c([H])c1[H]
+CMPD_0000000009	[H]Oc1c([H])c([H])c([H])c([H])c1[H]
+CMPD_0000000010	[H]OC(=O)c1c([H])c([H])c(O[H])c(O[H])c1[H]
+CMPD_0000000015	[H]OC(=O)c1c([H])c([H])c(N([H])O[H])c([H])c1[H]
+CMPD_0000000020	[H]OC(=NC([H])([H])C([H])([H])SC(=O)c1c([H])c([H])c([H])c([H])c1[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H]
+CMPD_0000000025	[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1[H]
+CMPD_0000000028	[H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H]
+MNXM1	[H+]
+MNXM01	[H+]
+MNXM10	[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]
+MNXM11	[H]OP(=O)(O[H])OP(=O)(O[H])O[H]
+MNXM1132	[H]OC(=O)C([H])([H])C([H])([H])C(=O)c1c([H])c([H])c([H])c([H])c1C(=O)SC([H])([H])C([H])([H])N=C(O[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H]
+MNXM12	[H]OC(=NC([H])([H])C([H])([H])S[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H]
+MNXM164	[H]OC(=O)c1c([H])c([H])c(O[H])c([H])c1[H]
+MNXM188	[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]
+MNXM2	[H]O[H]
+MNXM25	[H]OC(=O)C([H])([H])C([H])([H])C(=O)O[H]
+MNXM337	[H]OC(=O)C(OC1([H])C([H])=C(C(=O)O[H])C([H])=C([H])C1([H])O[H])=C([H])[H]
+MNXM4	O=O
+MNXM421	[H]OC(=O)c1c([H])c([H])c(N([H])[H])c([H])c1[H]
+MNXM438	[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]
+MNXM455	[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1O[H]
+MNXM473	[H]C(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]
+MNXM497	[H]OC(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]
+MNXM6	[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]
+MNXM611	[H]OC(=O)C1=C([H])C(=O)C([H])(O[H])C([H])(O[H])C1([H])[H]
+MNXM76	[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c(O[H])c([H])c1[H]
+MNXM799	[H]OC(=O)C(OC1([H])C([H])=C([H])C([H])=C(C(=O)O[H])C1([H])O[H])=C([H])[H]
+TARGET_0000000001	[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]

tools/rptools/test-data/4-rp2paths_pathways.csv

@@ -1,10 +1,96 @@
 "Path ID","Unique ID","Rule ID","Left","Right"
-"1","TRS_0_0_1_0","RR-02-ae41ec5771136ea5-14-F","1.CMPD_0000000001","1.TARGET_0000000001"
-"1","TRS_0_1_9_0","RR-02-bedda4e2f5001e0c-14-F","1.CMPD_0000000003","1.CMPD_0000000001"
-"1","TRS_0_2_739_0","RR-02-90bcfd187709eb1b-14-F","1.MNXM132:1.MNXM83","1.CMPD_0000000003"
-"2","TRS_0_0_1_0","RR-02-ae41ec5771136ea5-14-F","1.CMPD_0000000001","1.TARGET_0000000001"
-"2","TRS_0_1_9_0","RR-02-bedda4e2f5001e0c-14-F","1.CMPD_0000000003","1.CMPD_0000000001"
-"2","TRS_0_2_740_0","RR-02-0c33a3bfd9bf5ad5-14-F,RR-02-6692e4af37fbca2d-14-F","1.MNXM100:1.MNXM83","1.CMPD_0000000003"
-"3","TRS_0_0_1_0","RR-02-ae41ec5771136ea5-14-F","1.CMPD_0000000001","1.TARGET_0000000001"
-"3","TRS_0_1_9_0","RR-02-bedda4e2f5001e0c-14-F","1.CMPD_0000000003","1.CMPD_0000000001"
-"3","TRS_0_2_742_0","RR-02-07adee9ac9c42c7d-14-F,RR-02-1494429c7e6e0694-14-F,RR-02-1d50852f3f343682-14-F,RR-02-3bf131230c6b2bf2-14-F,RR-02-58d0f0d25e47b74a-14-F,RR-02-b3db29f084fc7a81-14-F,RR-02-f9759fe03c57b29f-14-F","1.MNXM34:1.MNXM83","1.CMPD_0000000003"
+"1","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"1","TRS_0_1_2_0","RR-02-9137e79005134eeb-16-F","1.MNXM188:1.MNXM4:1.MNXM6","1.CMPD_0000000003"
+"2","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"2","TRS_0_1_20_0","RR-02-876f09a1ab1b55e5-16-F","1.MNXM455","1.CMPD_0000000003"
+"3","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"3","TRS_0_1_9_0","RR-02-f145fec21961a59d-16-F","1.MNXM10:1.MNXM188:1.MNXM4","1.CMPD_0000000003"
+"4","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"4","TRS_0_1_11_0","RR-02-1982e8dd17b0357f-16-F","1.CMPD_0000000008:1.MNXM10:1.MNXM4","1.CMPD_0000000003"
+"4","TRS_0_2_42_0","RR-02-56602d66630bcfc3-16-F","1.MNXM2:1.MNXM438","1.CMPD_0000000008"
+"5","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"5","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003"
+"5","TRS_0_2_58_0","RR-02-7a379131479b23f9-16-F","1.MNXM76","1.CMPD_0000000009"
+"6","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"6","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003"
+"6","TRS_0_2_59_0","RR-02-a51b7d91cd2e9c7b-16-F","1.MNXM2:1.MNXM497","1.CMPD_0000000009"
+"7","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"7","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003"
+"7","TRS_0_2_60_0","RR-02-d3b162f199b260fc-16-F","1.MNXM164","1.CMPD_0000000009"
+"8","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"8","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003"
+"8","TRS_0_2_58_0","RR-02-7a379131479b23f9-16-F","1.MNXM76","1.CMPD_0000000009"
+"9","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"9","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003"
+"9","TRS_0_2_59_0","RR-02-a51b7d91cd2e9c7b-16-F","1.MNXM2:1.MNXM497","1.CMPD_0000000009"
+"10","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"10","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003"
+"10","TRS_0_2_60_0","RR-02-d3b162f199b260fc-16-F","1.MNXM164","1.CMPD_0000000009"
+"11","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"11","TRS_0_1_3_0","RR-02-217503934671e143-16-F","1.CMPD_0000000009:1.MNXM4:1.MNXM6","1.CMPD_0000000003"
+"11","TRS_0_2_58_0","RR-02-7a379131479b23f9-16-F","1.MNXM76","1.CMPD_0000000009"
+"12","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"12","TRS_0_1_3_0","RR-02-217503934671e143-16-F","1.CMPD_0000000009:1.MNXM4:1.MNXM6","1.CMPD_0000000003"
+"12","TRS_0_2_59_0","RR-02-a51b7d91cd2e9c7b-16-F","1.MNXM2:1.MNXM497","1.CMPD_0000000009"
+"13","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"13","TRS_0_1_3_0","RR-02-217503934671e143-16-F","1.CMPD_0000000009:1.MNXM4:1.MNXM6","1.CMPD_0000000003"
+"13","TRS_0_2_60_0","RR-02-d3b162f199b260fc-16-F","1.MNXM164","1.CMPD_0000000009"
+"14","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"14","TRS_0_1_19_0","RR-02-9bcd062586f04b0c-16-F","1.CMPD_0000000010","1.CMPD_0000000003"
+"14","TRS_0_2_10_0","RR-02-1569dbad49850632-16-F","1.MNXM611","1.CMPD_0000000010"
+"15","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"15","TRS_0_1_19_0","RR-02-9bcd062586f04b0c-16-F","1.CMPD_0000000010","1.CMPD_0000000003"
+"15","TRS_0_2_3_0","RR-02-71e589efe3bf9cc4-16-F","1.MNXM1:1.MNXM4:1.MNXM421","1.CMPD_0000000010"
+"16","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"16","TRS_0_1_19_0","RR-02-9bcd062586f04b0c-16-F","1.CMPD_0000000010","1.CMPD_0000000003"
+"16","TRS_0_2_4_0","RR-02-ca843b65c26614a8-16-F,RR-02-dbeb51ef1cde8f29-16-F","1.MNXM164:1.MNXM4:1.MNXM6","1.CMPD_0000000010"
+"17","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
+"17","TRS_0_1_19_0","RR-02-9bcd062586f04b0c-16-F","1.CMPD_0000000010","1.CMPD_0000000003"
+"17","TRS_0_2_6_0","RR-02-82a5e24712957f97-16-F","1.MNXM10:1.MNXM164:1.MNXM4","1.CMPD_0000000010"
+"18","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001"
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