--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pcdl_get_conc_df.xml	Mon Aug 04 19:00:39 2025 +0000
@@ -0,0 +1,93 @@
+<tool id="pcdl_get_conc_df" name="pcdl_get_conc_df" 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_conc_df 'output_pc' $entropy
+        --verbose $verbose
+        --drop $drop
+        --keep $keep
+        --collapse $collapse
+    ]]></command>
+    <inputs>
+        <section name="essential" title="essential:" expanded="true">
+            <expand macro="path"/>
+            <expand macro="entropy"/>
+            <expand macro="drop"/>
+            <expand macro="keep"/>
+            <expand macro="collapse"/>
+        </section>
+        <section name="advanced" title="advanced:" expanded="false">
+            <expand macro="verbose"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="conc_csv" type="list">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+_conc)\.csv" format="csv" directory="output_pc" visible="false"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <section name="essential">
+                <param name="path">
+                    <expand macro="output"/>
+                </param>
+                <param name="collapse" value="true"/>
+            </section>
+            <section name="advanced">
+                <param name="verbose" value="true"/>
+            </section>
+            <output_collection name="conc_csv" count="1">
+                <element name="timeseries_conc">
+                    <assert_contents>
+                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p"/>
+                        <has_text text=",time,runtime,xmlfile"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <section name="essential">
+                <param name="path">
+                    <expand macro="output"/>
+                </param>
+                <param name="collapse" value="false"/>
+            </section>
+            <section name="advanced">
+                <param name="verbose" value="false"/>
+            </section>
+            <output_collection name="conc_csv" count="2">
+                <element name="output00000000_conc">
+                    <assert_contents>
+                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
+                        <has_text text=",time,runtime,xmlfile"/>
+                    </assert_contents>
+                </element>
+                <element name="output00000001_conc">
+                    <assert_contents>
+                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
+                        <has_text text=",time,runtime,xmlfile"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+This function extracts dataframes with concentration values for all chemical species in all voxels and saves them as csv files. Additionally, this dataframe lists voxel and mesh center coordinates.
+
+Homepage: https://github.com/elmbeech/physicelldataloader
+    ]]></help>
+    <citations>
+        <expand macro="citation"/>
+    </citations>
+</tool>