--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyzing-model.xml	Sun Oct 02 19:27:06 2022 +0000
@@ -0,0 +1,97 @@
+<tool id="straindesign_analyzing_model" name="StrainDesign analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
+    <description>Produce a pareto plot for a biological model</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## Run cmdline
+        python -m straindesign analyzing-model
+            @CMD_INPUT_MODEL@
+            @CMD_INPUT_MEDIUM@
+            @CMD_BIOMASS_RXN_ID@
+            @CMD_TARGET_RXN_ID@
+            @CMD_INPUT_PATHWAY@
+            #if str('$substrate_cond.substrate_param') == 'yes'
+                --substrate-rxn-id '$substrate_cond.substrate_rxn_id'
+            #end if
+            --output-pareto-png '$output_png'
+    ]]></command>
+    <expand macro="env_variables"/>
+    <inputs>
+        <expand macro="input_model_sbml"/>
+        <expand macro="input_medium_tsv"/>
+        <expand macro="input_biomass_rxn_id"/>
+        <expand macro="input_target_rxn_id"/>
+        <expand macro="input_pathway_sbml"/>
+        <conditional name="substrate_cond">
+            <param name="substrate_param" type="select" label="Provide a substrate reaction" help="Choose yourself a carbon source or it will be detected automatically">
+                <option value="yes">yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <expand macro="input_substrate_rxn_id"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_png" format="png" label="${tool.name}" />
+    </outputs>
+    <tests>
+        <test>
+            <!--  test 1  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
+            <param name="target_rxn_id" value="EX_tyrp_e" />
+            <output name="output_png" ftype="png">
+                <assert_contents>
+                    <has_size value="34000" delta="4000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!--  test 2  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
+            <param name="target_rxn_id" value="EX_tyrp_e" />
+            <param name="substrate_rxn_id" value="EX_glc__D_e" />
+            <output name="output_png" ftype="png">
+                <assert_contents>
+                    <has_size value="34000" delta="4000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!--  test 3  -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
+            <param name="pathway" ftype="sbml" value="butanol.xml" />
+            <param name="medium" ftype="tabular" value="butanol.tsv" />
+            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
+            <param name="substrate_rxn_id" value="EX_glc__D_e" />
+            <param name="target_rxn_id" value="EX_1btol_e" />
+            <output name="output_png" ftype="png">
+                <assert_contents>
+                    <has_size value="34000" delta="4000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_TITLE@
+
+This tool produces a phenotypic-phase-plane plot given these datas:
+* model
+* reaction producing a target
+* biomass reaction
+These informations are optionals and will be adapted to your needs:
+* an heterologous pathway
+* a carbon substrate
+* media composition
+
+@HELP_LINK@
+    ]]></help>
+    <expand macro="creator"/>
+    <expand macro="citation"/>
+</tool>