--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/simulate-deletion.xml	Mon May 15 14:05:52 2023 +0000
@@ -0,0 +1,96 @@
+<tool id="straindesign_simulate_deletion" name="StrainDesign simulate-deletion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
+    <description>Search genes to delete in a biological model</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m straindesign simulate-deletion
+            @CMD_INPUT_MODEL@
+            @CMD_INPUT_PATHWAY@
+            @CMD_INPUT_MEDIUM@
+            @CMD_BIOMASS_RXN_ID@
+            @CMD_TARGET_RXN_ID@
+            --strategy '$input_strategy.strategy'
+            #if str($input_strategy.strategy) == 'ko':
+                --substrate-rxn-id '$input_strategy.substrate_rxn_id'
+                #if $input_strategy.annotate:
+                    --email '$__user_email__'
+                #end if
+            #end if
+            #if str($max_time_cond.max_time_param) == 'yes':
+                --max-time '$max_time_cond.max_time'
+            #end if
+            --max-knockouts '$max_knockouts'
+            --output-file-tsv '$output_tsv'
+    ]]></command>
+    <expand macro="env_variables"/>
+    <inputs>
+        <expand macro="input_model_sbml"/>
+        <expand macro="input_pathway_sbml"/>
+        <expand macro="input_medium_tsv"/>
+        <expand macro="input_biomass_rxn_id"/>
+        <expand macro="input_target_rxn_id"/>
+        <conditional name="input_strategy">
+            <param name="strategy" type="select" label="Strategy" help="Genes or Reactions to delete">
+                <option value="ko" selected="True">Gene knockouts</option>
+                <option value="ou" >Reaction knockouts</option>
+            </param>
+            <when value="ko">
+                <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
+                    <validator type="empty_field" message="Substrate reaction ID is required"/>
+                    <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
+                </param>
+                <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Please agree to use your email for query the NCBI website to annotate the genes"/>
+            </when>
+            <when value="ou">
+            </when>
+        </conditional>
+        <param name="max_knockouts" type="integer" min="1" max="10" value="3" label="Number of items deleted to consider"/>
+        <conditional name="max_time_cond">
+            <param name="max_time_param" type="select" label="Time out" help="Limit scan time">
+                <option value="no" selected="True">no</option>
+                <option value="yes" >yes</option>
+            </param>
+            <when value="yes">
+                <param name="max_time" type="integer" min="5" max="120" value="10" label="minutes"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_tsv" format="tabular" label="${tool.name}(${input_strategy.strategy})" />
+    </outputs>
+    <tests>
+        <test>
+            <!--   test 1   -->
+            <param name="model" ftype="sbml" value="iAF1260.xml.gz" />
+            <param name="pathway" ftype="sbml" value="butanol.xml" />
+            <param name="medium" ftype="tabular" value="butanol.tsv" />
+            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
+            <param name="target_rxn_id" value="EX_1btol_e" />
+            <param name="substrate_rxn_id" value="EX_glc__D_e" />
+            <param name="max_time_param" value="yes"/>
+            <param name="max_time" value="5"/>
+            <output name="output_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="^reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness$"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_TITLE@
+
+This tool helps to identify gene's deletions in a biological model to optimize the reaction of a targeted compound.
+The medium composition can be modified with a TSV file formatted as following: no header, with these columns "reaction id, lower_bound, upper_bound".
+The strategies "ko" and "ou" find genes and reactions respectively to delete.
+
+Disclaimer: if you want to annotate the genes with their names, your email address will be used by the library Biopython to request the NCBI website.
+
+@HELP_LINK@
+    ]]></help>
+    <expand macro="creator"/>
+    <expand macro="citation"/>
+</tool>