diff pcdl_get_substrate_list.xml @ 0:d769482946e0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pcdl_get_substrate_list.xml	Mon Aug 04 18:58:10 2025 +0000
@@ -0,0 +1,57 @@
+<tool id="pcdl_get_substrate_list" name="pcdl_get_substrate_list" version="3.0.1+galaxy0" profile="21.05">
+    <macros>
+        <import>pcdl_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirement"/>
+    </requirements>
+    <command><![CDATA[
+        #import re
+        mkdir output_pc &&
+        #for $file in $path:
+            #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
+            ln -s '$file' output_pc/$filename &&
+        #end for
+
+        pcdl_get_substrate_list 'output_pc'
+        --verbose $verbose
+        > '$substrate_txt'
+    ]]></command>
+    <inputs>
+        <section name="essential" title="essential:" expanded="true">
+            <expand macro="path"/>
+        </section>
+        <section name="advanced" title="advanced:" expanded="false">
+            <expand macro="verbose"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="substrate_txt" label="substrate_txt" format="txt"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <section name="essential">
+                <param name="path">
+                    <expand macro="output"/>
+                </param>
+            </section>
+            <section name="advanced">
+                <param name="verbose" value="true"/>
+            </section>
+            <output name="substrate_txt">
+                <assert_contents>
+                    <has_text text="['"/>
+                    <has_text text="']"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This function is returns all chemical species names, modeled in the microenvironment, ordered by subsrate ID.
+
+Homepage: https://github.com/elmbeech/physicelldataloader
+    ]]></help>
+    <citations>
+        <expand macro="citation"/>
+    </citations>
+</tool>