--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fix.xml	Sun May 14 20:11:33 2023 +0000
@@ -0,0 +1,67 @@
+<tool id="cnvkit_fix" name="CNVkit Fix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Adjust raw coverage data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_target_file' ./tumor.targetcoverage.cnn &&
+        #if $input_antitarget_file
+            ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
+        #end if
+        #if $input_reference_coverage_file
+            ln -s '$input_reference_coverage_file' ./ref-tas.cnn &&
+        #end if
+        cnvkit.py fix
+            ./tumor.targetcoverage.cnn
+            #if $input_antitarget_file
+                ./tumor.antitargetcoverage.cnn
+            #end if  
+            #if $input_reference_coverage_file
+                ./ref-tas.cnn 
+            #end if  
+            --output sample.cnr
+            $cluster
+            #if $sample_id
+                --sample-id '$sample_id'
+            #end if
+            $no_gc
+            $no_edge
+            $no_rmask
+    ]]></command>
+    <inputs>
+        <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" />
+        <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" />
+        <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" />
+        <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
+        <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
+        <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
+        <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
+        <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
+    </inputs>
+    <outputs>
+        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+            <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" />
+            <param name="input_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" />
+            <param name="no_edge" value="1" />
+            <output name="out_sample_cnr">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output> 
+        </test>
+    </tests>
+    <help><![CDATA[
+        Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases
+        in regional coverage and GC content, according to the given reference.
+        
+        The reference .cnn file output contains those columns
+        chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
+        of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
+        depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
+    ]]></help>
+    <expand macro="citations" />
+</tool>