--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reference.xml	Sun May 14 20:11:55 2023 +0000
@@ -0,0 +1,178 @@
+<tool id="cnvkit_reference" name="CNVkit Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Compile a copy-number reference from the given files or directory containing normal samples</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        #import re
+        #if str($CNV_reference.CNV_reference_availabel) == "yes"
+            #set $names = []
+            #set $x=1
+            #for $x, $input in enumerate($CNV_reference.input_cnn_file):
+                #set $name_base = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
+                #set $name = $name_base + '_' + str(x)
+                #silent $names.append( $name )
+                ln -s '$input' ${name}.cnn  &&
+            #end for
+        #end if
+        #if str($CNV_reference.CNV_reference_availabel) == "no"
+            #if $CNV_reference.antitargets
+                ln -s '$CNV_reference.antitargets' ./antitargets.bed &&
+            #end if 
+            ln -s '$CNV_reference.targets' ./targets.bed &&
+        #end if
+        #if $CNV_reference.advanced_settings.reference_source.fasta
+            #if str($CNV_reference.advanced_settings.reference_source.ref_selector) == 'history':
+                ln -s '$CNV_reference.advanced_settings.reference_source.fasta' ./genome.fa &&
+                samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
+            #else
+                ln -s '$CNV_reference.advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
+                ln -s '${CNV_reference.advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
+            #end if
+        #end if
+        cnvkit.py reference
+            #if str($CNV_reference.CNV_reference_availabel) == "yes"
+                #for $name in $names:
+                    ${name}.cnn
+                #end for
+            #end if
+            --output ref-tas.cnn
+            $CNV_reference.advanced_settings.cluster
+            #if str($CNV_reference.advanced_settings.min_cluster_size)
+                --min-cluster-size '$CNV_reference.advanced_settings.min_cluster_size'
+            #end if
+            #if str($CNV_reference.advanced_settings.Sample_sex.sex) == "yes":
+                #if '$CNV_reference.advanced_settings.Sample_sex.sample_sex' == "Male"
+                    #set $sample_sex_val = "Male"
+                    --sample-sex '$segment_method_val'
+                #else
+                    --sample-sex '$CNV_reference.advanced_settings.Sample_sex.sample_sex'
+                #end if
+            #end if
+            $CNV_reference.advanced_settings.male_reference
+            #if str($CNV_reference.CNV_reference_availabel) == "no"
+                --targets ./targets.bed
+                #if $CNV_reference.antitargets
+                    --antitargets ./antitargets.bed
+                #end if
+            #end if
+            $CNV_reference.disable_some_of_the_bias_corrections.no_gc
+            $CNV_reference.disable_some_of_the_bias_corrections.no_edge
+            $CNV_reference.disable_some_of_the_bias_corrections.no_rmask
+    ]]></command>
+    <inputs>
+        <conditional name="CNV_reference">
+            <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file cnn?" help="">
+                <option value="no" selected="True">Build a new copy number reference file</option>
+                <option value="yes">Reuse a copy number reference file</option>
+            </param>
+            <when value="no">
+                <expand macro="construct_CNV_ref_with_natural_expected_number" />
+                <section name="advanced_settings" title="Advanced settings" expanded="false">
+                    <expand macro="reference_interface" />
+                    <expand macro="reference_optional" /> 
+                    <expand macro="sample_sex_condition" />
+                </section>
+                <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
+                    <expand macro="disable_specific_automatic_bias_corrections" />
+                </section>
+            </when>
+            <when value="yes">
+                <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="cnn file" help="Normal-sample target or antitarget cnn files, or the directory that contains them" />
+                <section name="advanced_settings" title="Advanced settings" expanded="false">
+                    <expand macro="reference_interface" />
+                    <expand macro="reference_optional" />
+                    <conditional name="Sample_sex">
+                        <param name="sex" type="select" label="Sample sex availabel" help="">
+                            <option value="yes">Select sample sex</option>
+                        </param>
+                        <when value="yes">
+                            <expand macro="sample_sex" />
+                        </when>
+                    </conditional>
+                </section>
+                <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
+                    <expand macro="disable_specific_automatic_bias_corrections" />
+                </section>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="history"/>
+                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <param name="CNV_reference_availabel" value="yes" />
+            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+            <param name="no_gc" value="1" />
+            <output name="out_referene_tas" file="ref-tas.cnn" /> 
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <param name="CNV_reference_availabel" value="yes" />
+            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+            <param name="no_gc" value="1" />
+            <output name="out_referene_tas" file="ref-tas.cnn" />
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <param name="CNV_reference_availabel" value="yes" />
+            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,sample.targetcoverage.cnn" />
+            <param name="no_gc" value="1" />
+            <output name="out_referene_tas">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <param name="CNV_reference_availabel" value="no" />
+            <param name="targets" ftype="bed" value="capture.target.bed" />
+            <param name="no_gc" value="1" />
+            <output name="out_referene_tas">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <conditional name="Sample_sex">
+                <param name="sex" value="yes" />
+            </conditional>
+            <param name="CNV_reference_availabel" value="no" />
+            <param name="targets" ftype="bed" value="capture.target.bed" />
+            <param name="no_gc" value="1" />
+            <output name="out_referene_tas">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+    Compile a copy-number reference from the given files or directory (containing normal samples).
+    If given a reference genome (-f option), also calculate the GC content and repeat-masked
+    proportion of each region.
+    
+    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>