--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon May 15 14:05:52 2023 +0000
@@ -0,0 +1,97 @@
+<macros>
+    <!--  GLOBAL  -->
+    <token name="@TOOL_VERSION@">3.2.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@LICENSE@">MIT</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="WARNING" level="warning" />
+            <regex match="ERROR" level="fatal" />
+        </stdio>
+    </xml>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/s41467-022-32661-x</citation>
+        </citations>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+        </creator>
+    </xml>
+    <xml name="env_variables">
+        <environment_variables>
+            <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+            <environment_variable name="USERNAME">\$__user_email__</environment_variable>
+        </environment_variables>
+    </xml>
+
+    <!--  CMDLINE  -->
+<token name="@CMD_INPUT_MODEL@"><![CDATA[
+--input-model-file '$model'
+]]></token>
+<token name="@CMD_INPUT_PATHWAY@"><![CDATA[
+#if $pathway
+--input-pathway-file '$pathway'
+#end if
+]]></token>
+<token name="@CMD_INPUT_MEDIUM@"><![CDATA[
+#if $medium
+    --input-medium-file '$medium'
+#end if
+]]></token>
+<token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[
+--biomass-rxn-id '$biomass_rxn_id'
+]]></token>
+<token name="@CMD_TARGET_RXN_ID@"><![CDATA[
+--target-rxn-id '$target_rxn_id'
+]]></token>
+
+    <!--  INPUT  -->
+    <xml name="input_model_sbml">
+        <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/>
+    </xml>
+    <xml name="input_pathway_sbml">
+        <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/>
+    </xml>
+    <xml name="input_medium_tsv">
+        <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/>
+    </xml>
+    <xml name="input_biomass_rxn_id">
+        <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters">
+            <validator type="empty_field" message="Biomass reaction ID is required"/>
+            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
+        </param>
+    </xml>
+    <xml name="input_target_rxn_id">
+        <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters">
+            <validator type="empty_field" message="Target reaction ID is required"/>
+            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
+        </param>
+    </xml>
+    <xml name="input_substrate_rxn_id">
+        <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
+            <validator type="empty_field" message="Target reaction ID is required"/>
+            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
+        </param>
+    </xml>
+
+    <!--  HELP -->
+<token name="@HELP_TITLE@"><![CDATA[
+StrainDesign
+============
+]]></token>
+<token name="@HELP_LINK@"><![CDATA[
+Project Links
+-------------
+
+* `straindesign <https://github.com/brsynth/straindesign>`_
+* `cameo <https://github.com/biosustain/cameo>`_
+]]></token>
+</macros>