--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/autobin.xml	Sun May 14 20:05:09 2023 +0000
@@ -0,0 +1,125 @@
+<tool id="cnvkit_autobin" name="CNVkit Autobin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Estimates read counts or depths in a BAM file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        #import re
+        #set $names = []
+        #set $x=1
+        #for $x, $bam in enumerate($bams):
+            #set $name_base = re.sub('[^\w\-_\.]', '_', $bam.element_identifier)
+            #set $name = $name_base + '_' + str(x)
+            #silent $names.append( $name )
+            ln -s '$bam' ${name}.bam  &&
+            ln -s '${bam.metadata.bam_index}' ${name}.bai  &&
+        #end for
+        ln -s '$targets' ./capture.bed &&
+        #if $advanced_settings.reference_source.fasta
+            #if str($advanced_settings.reference_source.ref_selector) == 'history':
+                ln -s '$advanced_settings.reference_source.fasta' ./genome.fa &&
+                samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
+            #else
+                ln -s '$advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
+                ln -s '${advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
+            #end if
+        #end if
+        #if $advanced_settings.access
+            ln -s '$advanced_settings.access' ./access.bed &&
+        #end if
+        #if $advanced_settings.annotate
+            ln -s '$advanced_settings.annotate' ./annotate.bed &&
+        #end if
+        #if $advanced_settings.target_output_bed
+            ln -s '$advanced_settings.target_output_bed' ./target_output.bed &&
+        #end if
+        #if $advanced_settings.antitarget_output_bed
+            ln -s '$advanced_settings.antitarget_output_bed' ./antitarget_output.bed &&
+        #end if
+        cnvkit.py autobin
+            #for $name in $names:
+                ${name}.bam
+            #end for
+            --targets ./capture.bed
+            #if $advanced_settings.method == "hybrid"
+                #set $method_val = "hybrid"
+                --method '$method_val'
+            #else
+                --method '$method'
+           #end if
+           #if $advanced_settings.access
+               --access ./access.bed
+           #end if
+           #if str($advanced_settings.bp_per_bin)
+               --bp-per-bin $advanced_settings.bp_per_bin
+           #end if
+           #if str($advanced_settings.target_max_size)
+               --target-max-size $advanced_settings.target_max_size
+           #end if
+           #if str($advanced_settings.target_min_size)
+               --target-min-size $advanced_settings.target_min_size
+           #end if
+           #if str($advanced_settings.antitarget_max_size)
+               --antitarget-max-size $advanced_settings.antitarget_max_size
+           #end if
+           #if str($advanced_settings.antitarget_min_size)
+               --antitarget-min-size $advanced_settings.antitarget_min_size
+           #end if
+           #if $advanced_settings.annotate
+               --annotate ./annotate.bed
+           #end if
+           $advanced_settings.short_names
+           #if $advanced_settings.target_output_bed
+                --target-output-bed ./target_output.bed
+           #end if
+           #if $advanced_settings.antitarget_output_bed
+                --antitarget-output-bed ./antitarget_output.bed
+           #end if
+    ]]></command>
+    <inputs>
+        <param name="bams" type="data" multiple="true" format="bam" label="Input Sample BAM file/s" help="" />
+        <param argument="--targets" type="data" format="bed,tabular" label="Input Potentially targeted genomic regions" help="e.g. all possible exons for the reference genome. Format: BED, interval list, etc." />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <expand macro="reference_interface" />
+            <expand macro="autobin_optional" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture target" from_work_dir="capture.target.bed" />
+        <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture antitarget" from_work_dir="capture.antitarget.bed" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="history"/>
+                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <param name="bams" ftype="bam" value="tumor.bam" />
+            <param name="targets" ftype="bed" value="capture.bed" />
+            <output name="out_capture_target" file="capture.target.bed" /> 
+            <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <param name="bams" ftype="bam" value="tumor.bam" />
+            <param name="targets" ftype="bed" value="capture.bed" />
+            <output name="out_capture_target" file="capture.target.bed" /> 
+            <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 
+        </test>
+        <test expect_num_outputs="2">
+            <param name="bams" ftype="bam" value="tumor.bam,tumor_1.bam" />
+            <param name="targets" ftype="bed" value="capture.bed" />
+            <output name="out_capture_target" file="capture.target.bed" /> 
+            <output name="out_capture_antitarget" file="multible_capture.antitarget.bed" /> 
+        </test>
+    </tests>
+    <help><![CDATA[
+         Quickly estimate read counts or depths in a BAM file to estimate reasonable on- and (if relevant) off-target bin sizes.
+    ]]></help>
+    <expand macro="citations" />
+</tool>