--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pcdl_plot_scatter.xml	Mon Aug 04 18:59:56 2025 +0000
@@ -0,0 +1,102 @@
+<tool id="pcdl_plot_scatter" name="pcdl_plot_scatter" 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_plot_scatter 'output_pc' '$focus_cell'
+        --custom_data_type $custom_data_type
+        --microenv $microenv
+        --physiboss $physiboss
+        --settingxml 'none'
+        --verbose $verbose
+        --z_slice $z_slice
+        --z_axis '$z_axis'
+        --alpha $alpha
+        --cmap '$cmap'
+        --title '$title'
+        --grid $grid
+        --legend_loc '$legend_loc'
+        --xlim '$xlim'
+        --ylim '$ylim'
+        --xyequal $xyequal
+        --s $s
+        --figsizepx $figsizepx_x $figsizepx_y
+        --directory 'jakku'
+        --ext $ext
+        --figbgcolor '$figbgcolor'
+    ]]></command>
+    <inputs>
+        <section name="essential" title="essential:" expanded="true">
+            <expand macro="path"/>
+            <expand macro="focus_cell"/>
+            <expand macro="custom_data_type"/>
+            <expand macro="z_slice"/>
+            <expand macro="z_axis"/>
+            <expand macro="alpha"/>
+            <expand macro="cmap"/>
+            <expand macro="title"/>
+            <expand macro="grid"/>
+            <expand macro="legend_loc"/>
+            <expand macro="xlim"/>
+            <expand macro="ylim"/>
+            <expand macro="xyequal"/>
+            <expand macro="s"/>
+            <expand macro="figsizepx_x"/>
+            <expand macro="figsizepx_y"/>
+            <expand macro="ext"/>
+            <expand macro="figbgcolor"/>
+        </section>
+        <section name="advanced" title="advanced:" expanded="false">
+            <expand macro="microenv"/>
+            <expand macro="physiboss"/>
+            <expand macro="verbose"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="scatter_plot" type="list">
+            <discover_datasets pattern="(?P&lt;designation&gt;output.+)\.jpeg" format="jpg" directory="jakku" visible="false"/>
+        </collection>
+    </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="false"/>
+            </section>
+            <output_collection name="scatter_plot" count="2">
+                <element name="output00000000_cell_type">
+                    <assert_contents>
+                        <has_text text="JFIF"/>
+                    </assert_contents>
+                </element>
+                <element name="output00000001_cell_type">
+                    <assert_contents>
+                        <has_text text="JFIF"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Function generates pandas scatter plots.
+
+Homepage: https://github.com/elmbeech/physicelldataloader
+    ]]></help>
+    <citations>
+        <expand macro="citation"/>
+    </citations>
+</tool>