diff gem_macros.xml @ 0:d9893d41dd6a draft default tip

planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gem_macros.xml	Fri Dec 13 21:33:34 2024 +0000
@@ -0,0 +1,75 @@
+<macros>
+    <!-- Tokens -->
+    <token name="@VERSION@">0.29.1</token>
+    <token name="@PROFILE@">23.0</token>
+    
+    <!-- Add version commands for different tools -->
+    <xml name="version_command_cobra">
+        <version_command>echo '@VERSION@'</version_command>
+    </xml>
+    
+    <xml name="version_command_escher">
+        <version_command>python -c 'from escher import __version__; print(__version__)'</version_command>
+    </xml>
+
+    <xml name="version_command_memote">
+        <version_command>python -c 'from memote import __version__; print(__version__)'</version_command>
+    </xml>
+    
+    <!-- Version command uses cobra requirement version -->
+    <xml name="version_command">
+        <version_command>echo '@VERSION@'</version_command>
+    </xml>
+
+    <!-- Setting cobra requirement to use version token -->
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cobra</requirement>
+            <requirement type="package" version="2.2.3">pandas</requirement>
+            <requirement type="package" version="0.17.0">memote</requirement>
+            <requirement type="package" version="1.7.3">escher</requirement>
+        </requirements>
+    </xml>
+
+    <!-- Common inputs -->
+    <xml name="input_model">
+        <param format="sbml" name="cb_model_location" type="data" label="Model to analyze"/>
+    </xml>
+
+    <xml name="input_uptake_constraints">
+        <param format="csv" name="uptake_constraints_file" type="data" label="Uptake constraints CSV file" optional="true"/>
+    </xml>
+
+    <!-- Common outputs -->
+    <xml name="output">
+        <data name="output" format="csv" label="${tool.name} on ${on_string}"/>
+    </xml>
+
+    <!-- Common test elements -->
+    <xml name="test_invalid_model">
+        <test expect_failure="true">
+            <param name="cb_model_location" value="invalid_format.txt"/>
+            <assert_stderr>
+                <has_text text="The model could not be read"/>
+            </assert_stderr>
+        </test>
+    </xml>
+
+    <!-- Citations -->
+    <xml name="citation_cobrapy">
+        <citation type="doi">10.1186/1752-0509-7-74</citation>
+    </xml>
+
+    <xml name="citation_pandas">
+        <citation type="doi">10.5281/zenodo.3509134</citation>
+    </xml>
+
+    <xml name="citation_escher">
+        <citation type="doi">10.1371/journal.pcbi.1004321</citation>
+    </xml>
+
+    <xml name="citation_memote">
+        <citation type="doi">10.1038/s41587-020-0446-y</citation>
+    </xml>
+
+</macros>