--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segment.xml	Sun May 14 20:07:45 2023 +0000
@@ -0,0 +1,83 @@
+<tool id="cnvkit_segment" name="CNVkit Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Infer copy number segments from the given coverage table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$filename' ./tumor.cnr &&
+        #if $additional_SNP_allelic_process.vcf
+            ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
+        #end if
+        #import os
+        cnvkit.py segment
+            ./tumor.cnr
+            --output sample.cns
+            --processes \${GALAXY_SLOTS:-4}
+            #if $advanced_settings.dataframe
+                --dataframe '$advanced_settings.dataframe'
+            #end if
+            #if $advanced_settings.method == "cbs"
+                #set $method_val = "cbs"
+                --method '$method_val'
+            #else
+                --method '$advanced_settings.method'
+            #end if
+            #if str($advanced_settings.threshold)
+                --threshold $advanced_settings.threshold
+            #end if
+            $advanced_settings.drop_low_coverage
+            #if str($advanced_settings.drop_outliers)
+                 --drop-outliers $advanced_settings.drop_outliers
+            #end if
+            $advanced_settings.smooth_cbs
+            #if $additional_SNP_allelic_process.vcf
+                 --vcf ./vcf_file.vcf
+            #end if
+            #if $additional_SNP_allelic_process.sample_id
+                --sample-id '$additional_SNP_allelic_process.sample_id'
+            #end if
+            #if $additional_SNP_allelic_process.normal_id
+                 --normal-id '$additional_SNP_allelic_process.normal_id'
+            #end if
+            #if str($additional_SNP_allelic_process.min_variant_depth)
+                 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
+            #end if
+            #if str($additional_SNP_allelic_process.zygosity_freq)
+                 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="filename" type="data" format="tabular" label="Input CNR file" help="" />
+        <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
+            <expand macro="additionally_SNP_process" />
+        </section>
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <expand macro="segment_optional" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_sample_segment" format="tabular" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="filename" ftype="tabular" value="tumor.cnr" />
+            <param name="method" value="hmm" />
+            <param name="threshold" value="2" />
+            <param name="drop_outliers" value="2" />
+            <param name="drop_low_coverage" value="1" />
+            <output name="out_sample_segment">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+         Infer copy number segments from the given coverage table. Segmentation runs independently on
+         each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
+         
+         Segmented log2 ratios (.cns) output file contains those columns
+          chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
+    ]]></help>
+    <expand macro="citations" />
+</tool>