--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatter.xml	Sun May 14 20:10:25 2023 +0000
@@ -0,0 +1,103 @@
+<tool id="cnvkit_scatter" name="CNVkit Scatter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Plot bin-level log2 coverages and segmentation calls together</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_cnr_file' ./tumor.cnr &&
+        #if $advanced_settings.segment
+        ln -s '$advanced_settings.segment' ./segment.cns &&
+        #end if
+        #if $advanced_settings.range_list
+            ln -s '$advanced_settings.range_list' ./list.bed &&
+        #end if
+        #if $advanced_settings.additional_SNP_allelic_process.vcf
+            ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
+        #end if
+        cnvkit.py scatter
+            ./tumor.cnr
+            --output sample-scatter.png
+            #if $advanced_settings.segment
+                --segment ./segment.cns
+            #end if
+            #if $advanced_settings.chromosome
+                --chromosome '$advanced_settings.chromosome'
+            #end if
+            #if $advanced_settings.gene
+                --gene '$advanced_settings.gene'
+            #end if
+            #if $advanced_settings.range_list
+                --range-list ./list.bed
+            #end if
+            #if str($advanced_settings.width)
+                --width  $advanced_settings.width
+            #end if
+            #if $advanced_settings.plot_aesthetics.antitarget_marker
+                --antitarget-marker '$advanced_settings.plot_aesthetics.antitarget_marker'
+            #end if
+            $advanced_settings.plot_aesthetics.by_bin
+            #if $advanced_settings.plot_aesthetics.segment_color
+                --segment-color '$advanced_settings.plot_aesthetics.segment_color'
+            #end if
+            #if $advanced_settings.plot_aesthetics.title
+                --title '$advanced_settings.plot_aesthetics.title'
+            #end if
+            $advanced_settings.plot_aesthetics.trend
+            #if str($advanced_settings.plot_aesthetics.y_max)
+                --y-max $advanced_settings.plot_aesthetics.y_max
+            #end if
+            #if str($advanced_settings.plot_aesthetics.y_min)
+                --y-min $advanced_settings.plot_aesthetics.y_min
+            #end if
+            #if str($advanced_settings.plot_aesthetics.fig_size)
+                --fig-size $advanced_settings.plot_aesthetics.fig_size
+            #end if
+            #if $advanced_settings.additional_SNP_allelic_process.vcf
+                --vcf ./vcf_file.vcf
+            #end if
+            #if $advanced_settings.additional_SNP_allelic_process.sample_id
+                --sample-id '$advanced_settings.additional_SNP_allelic_process.sample_id'
+            #end if
+            #if $advanced_settings.additional_SNP_allelic_process.normal_id
+                --normal-id '$advanced_settings.additional_SNP_allelic_process.normal_id'
+            #end if
+            #if str($advanced_settings.additional_SNP_allelic_process.min_variant_depth)
+                --min-variant-depth $advanced_settings.additional_SNP_allelic_process.min_variant_depth
+            #end if
+            #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
+                --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <expand macro="scatter_optional" />
+            <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
+              <expand macro="scatter_plot" />
+            </section>
+            <section name="additional_SNP_allelic_process" title="Plot aesthetics" expanded="false">
+              <expand macro="additionally_SNP_process" />
+            </section>
+        </section>   
+    </inputs>
+    <outputs>
+        <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
+            <param name="zygosity_freq" value="0.25" />
+            <param name="by_bin" value="1" />
+            <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
+                <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
+        this plots the genome-wide copy number in a form familiar to those who have used array CGH.
+    ]]></help>
+    <expand macro="citations" />
+</tool>