--- a/rpextractsink.xml	Mon Jan 03 15:34:21 2022 +0000
+++ b/rpextractsink.xml	Tue Jan 11 10:26:50 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rpExtractSink" name="Sink from SBML" version="5.11.1">
+<tool id="rpextractsink" name="Sink from SBML" version="5.11.1" profile="19.09">
     <description>Generate the RetroPath2.0 sink file from an SBML input</description>
     <requirements>
         <requirement type="package" version="5.11.1">rptools</requirement>
@@ -7,14 +7,8 @@
 		<regex match="Could not retreive any species in the compartment" level="fatal" />
 	</stdio>
     <command detect_errors="exit_code"><![CDATA[
-        #if str($input_strain_type.strain_type) == "BiGG":
-            curl http://bigg.ucsd.edu/static/models/$(input_strain_type.input).xml.gz --output $(input_strain_type.input).xml.gz;
-            python -m rptools.rpextractsink
-                $(input_strain_type.input).xml.gz
-        #else
-            python -m rptools.rpextractsink
-                $(input_strain_type.input)
-        #end if
+        python -m rptools.rpextractsink
+            '$input'
             '$sink'
             --compartment_id '$adv.compartment_id'
         #if str($adv.remove_dead_end) == "true":
@@ -22,83 +16,19 @@
         #end if
     ]]></command>
     <inputs>
-        <conditional name="input_strain_type">
-            <param name="strain_type" type="select" label="Input type">
-                <option value="BiGG" selected="true">BiGG database</option>
-                <option value="user">Custom file</option>
-            </param>
-            <when value="user">
-                <param name="input" type="data" format="sbml" optional="false" label="Strain" />
-            </when>
-            <when value="BiGG">
-                <param name="input" type="select" label="Strain">
-                    <option value="iCN718">(iCN718) Acinetobacter baumannii AYE</option>
-                    <option value="iYO844">(iYO844) Bacillus subtilis subsp. subtilis str. 168</option>
-                    <option value="iRC1080">(iRC1080) Chlamydomonas reinhardtii</option>
-                    <option value="iCN900">(iCN900) Clostridioides difficile 630</option>
-                    <option value="iHN637">(iHN637) Clostridium ljungdahlii DSM 13528</option>
-                    <option value="iCHOv1_DG44">(iCHOv1_DG44) Cricetulus griseus</option>
-                    <option value="iCHOv1">(iCHOv1) Cricetulus griseus</option>
-                    <option value="iAF1260b">(iAF1260b) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="iAF1260">(iAF1260) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="iML1515" selected="true">(iML1515) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="iJO1366">(iJO1366) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="iJR904">(iJR904) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="e_coli_core">(e_coli_core) Escherichia coli str. K-12 substr. MG1655</option>
-                    <option value="iAF987">(iAF987) Geobacter metallireducens GS-15</option>
-                    <option value="iIT341">(iIT341) Helicobacter pylori 26695</option>
-                    <option value="iAT_PLT_636">(iAT_PLT_636) Homo sapiens</option>
-                    <option value="Recon3D">(Recon3D) Homo sapiens</option>
-                    <option value="iAB_RBC_283">(iAB_RBC_283) Homo sapiens</option>
-                    <option value="RECON1">(RECON1) Homo sapiens</option>
-                    <option value="iYL1228">(iYL1228) Klebsiella pneumoniae subsp. pneumoniae MGH 78578</option>
-                    <option value="iNF517">(iNF517) Lactococcus lactis subsp. cremoris MG1363</option>
-                    <option value="iAF692">(iAF692) Methanosarcina barkeri str. Fusaro</option>
-                    <option value="iMM1415">(iMM1415) Mus musculus</option>
-                    <option value="iNJ661">(iNJ661) Mycobacterium tuberculosis H37Rv</option>
-                    <option value="iEK1008">(iEK1008) Mycobacterium tuberculosis H37Rv</option>
-                    <option value="iLB1027_lipid">(iLB1027_lipid) Phaeodactylum tricornutum CCAP 1055/1</option>
-                    <option value="iAM_Pb448">(iAM_Pb448) Plasmodium berghei</option>
-                    <option value="iAM_Pc455">(iAM_Pc455) Plasmodium cynomolgi strain B</option>
-                    <option value="iAM_Pf480">(iAM_Pf480) Plasmodium falciparum 3D7</option>
-                    <option value="iAM_Pk459">(iAM_Pk459) Plasmodium knowlesi strain H</option>
-                    <option value="iAM_Pv461">(iAM_Pv461) Plasmodium vivax Sal-1</option>
-                    <option value="iJN746">(iJN746) Pseudomonas putida KT2440</option>
-                    <option value="iJN1463">(iJN1463) Pseudomonas putida KT2440</option>
-                    <option value="iND750">(iND750) Saccharomyces cerevisiae S288C</option>
-                    <option value="iMM904">(iMM904) Saccharomyces cerevisiae S288C</option>
-                    <option value="STM_v1_0">(STM_v1_0) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2</option>
-                    <option value="iYS1720">(iYS1720) Salmonella pan-reactome</option>
-                    <option value="iSB619">(iSB619) Staphylococcus aureus subsp. aureus N315</option>
-                    <option value="iYS854">(iYS854) Staphylococcus aureus subsp. aureus USA300_TCH1516</option>
-                    <option value="iJB785">(iJB785) Synechococcus elongatus PCC 7942</option>
-                    <option value="iJN678">(iJN678) Synechocystis sp. PCC 6803</option>
-                    <option value="iSynCJ816">(iSynCJ816) Synechocystis sp. PCC 6803</option>
-                    <option value="iLJ478">(iLJ478) Thermotoga maritima MSB8</option>
-                    <option value="iIS312">(iIS312) Trypanosoma cruzi Dm28c</option>
-                    <option value="iIS312_Trypomastigote">(iIS312_Trypomastigote) Trypanosoma cruzi Dm28c</option>
-                    <option value="iIS312_Epimastigote">(iIS312_Epimastigote) Trypanosoma cruzi Dm28c</option>
-                    <option value="iIS312_Amastigote">(iIS312_Amastigote) Trypanosoma cruzi Dm28c</option>
-                </param>
-            </when>
-        </conditional>
-        <!-- <param name="input" type="data" format="sbml" optional="false" label="SBML model" /> -->
+        <param name="input" type="data" format="xml" optional="false" label="Strain" />
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="compartment_id" type="text" value="c" label="SBML compartment ID" />
             <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
         </section>
     </inputs>
     <outputs>
-        <data name="sink" format="csv" label="${tool.name} - ${input_strain_type.input}" />
+        <data name="sink" format="csv" label="${tool.name} - ${input.name}" />
     </outputs>
     <tests>
         <test>
-        <!-- test 1: check if identical outputs are produced with default parameters  -->
-            <conditional name="input_strain_type">
-                <param name="strain_type" value="user"/>
-                <param name="input" value="E.coli.sbml" />
-            </conditional>
-            <param name="compartment_id" value="MNXC3"/>
+        <!-- test 1: check if identical outputs are produced with iCN718 model input  -->
+            <param name="input" value="iCN718.xml.gz" />
             <output name="sink" file="sink.csv" ftype="csv" compare="diff"/>
         </test>
     </tests>
@@ -131,7 +61,6 @@
 
 * **output_sink**\ : (string) Path to the output csv file
 
-
 Project Links
 ---------------------
 
@@ -140,13 +69,11 @@
 Version
 ----------
 
-5.9.2
-
+5.11.1
 
 Authors
 -------
 
-
 * **Melchior du Lac**
 * Joan Hérisson
 
@@ -158,58 +85,13 @@
 Acknowledgments
 ---------------
 
-
 * Thomas Duigou
 
-
-
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@article{le2005minimum,
-  title={Minimum information requested in the annotation of biochemical models (MIRIAM)},
-  author={Le Nov{\`e}re, Nicolas and Finney, Andrew and Hucka, Michael and Bhalla, Upinder S and Campagne, Fabien and Collado-Vides, Julio and Crampin, Edmund J and Halstead, Matt and Klipp, Edda and Mendes, Pedro and others},
-  journal={Nature biotechnology},
-  volume={23},
-  number={12},
-  pages={1509--1515},
-  year={2005},
-  publisher={Nature Publishing Group}
-}
-        </citation>
-        <citation type="bibtex">
-@article{delepine2018retropath2,
-  title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers},
-  author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
-  journal={Metabolic engineering},
-  volume={45},
-  pages={158--170},
-  year={2018},
-  publisher={Elsevier}}
-        </citation>
-        <citation type="bibtex">
-@article{ebrahim2013cobrapy,
-  title={COBRApy: COnstraints-based reconstruction and analysis for python},
-  author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
-  journal={BMC systems biology},
-  volume={7},
-  number={1},
-  pages={74},
-  year={2013},
-  publisher={Springer}
-}
-        </citation>
-        <citation type="bibtex">
-@article{bornstein2008libsbml,
-  title={LibSBML: an API library for SBML},
-  author={Bornstein, Benjamin J and Keating, Sarah M and Jouraku, Akiya and Hucka, Michael},
-  journal={Bioinformatics},
-  volume={24},
-  number={6},
-  pages={880--881},
-  year={2008},
-  publisher={Oxford University Press}
-}
-        </citation>
+        <citation type="doi">10.1038/nbt1156</citation>
+        <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
+        <citation type="doi">10.1186/1752-0509-7-74</citation>
+        <citation type="doi">10.1093/bioinformatics/btn051</citation>
     </citations>
 </tool>
\ No newline at end of file