--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/access.xml	Sun May 14 20:09:17 2023 +0000
@@ -0,0 +1,61 @@
+<tool id="cnvkit_access" name="CNVkit Access"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Calculate the sequence-accessible coordinates in chromosomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        #import re
+        ln -s '$fa_fname' ./genome.fasta &&
+        #if $exclude
+            #set $names = []
+            #set $x=1
+            #for $x, $exc in enumerate($exclude):
+                #set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier)
+                #set $name = $name_base + '_' + str(x)
+                #silent $names.append( $name )
+                ln -s '$exc' ${name}.bed  &&
+            #end for
+        #end if
+        cnvkit.py access
+            ./genome.fasta
+            #if $exclude
+                #for $name in $names:
+                    --exclude  ${name}.bed
+               #end for
+            #end if
+            #if str($min_gap_size)
+                --min-gap-size $min_gap_size
+            #end if
+            --output access-excludes.bed
+    ]]></command>
+    <inputs>
+        <param name="fa_fname" type="data" format="fasta" label="Target coverage file" help="Reference genome fasta file" />
+        <param argument="--min-gap-size" optional="true" type="integer" label="Minimum gap size between accessible sequence regions" min="0" value="5000" help="Regions separated by less than this distance will be joined together" />
+        <param argument="--exclude" type="data" optional="true" format="bed" multiple="true" label="Additional regions to exclude" help="" />
+    </inputs>
+    <outputs>
+        <data name="out_sample_access" format="bed" label="${tool.name} on ${on_string}: Sequence-accessible coordinates" from_work_dir="access-excludes.bed" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="fa_fname" ftype="fasta" value="genome.fasta" />
+            <param name="min_gap_size" value="2500" />
+            <param name="exclude" ftype="bed" value="excludes.bed" />
+            <output name="out_sample_access" file="access-excludes.bed" /> 
+        </test>
+        <test expect_num_outputs="1">
+            <param name="fa_fname" ftype="fasta" value="genome.fasta" />
+            <param name="min_gap_size" value="2500" />
+            <param name="exclude" ftype="bed" value="excludes.bed,excludes_1.bed" />
+            <output name="out_sample_access" file="access-excludes.bed" /> 
+        </test>
+    </tests>
+    <help><![CDATA[
+           The access command computes the locations of the accessible sequence regions for a given reference genome
+           based on these masked-out sequences, treating long spans of ‘N’ characters as the inaccessible regions
+           and outputting the coordinates of the regions between them.
+    ]]></help>
+    <expand macro="citations" />
+</tool>