diff antitarget.xml @ 0:98086253a782 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/antitarget.xml	Sun May 14 20:08:55 2023 +0000
@@ -0,0 +1,47 @@
+<tool id="cnvkit_antitarget" name="CNVkit Antitarget" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>lists the chromosomal coordinates for targeted resequencing</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$targets_file' ./capture.bed &&
+        #if $access
+            ln -s '$access' ./access.bed &&
+        #end if
+        cnvkit.py antitarget
+            ./capture.bed
+            #if $access
+                --access ./access.bed
+            #end if
+            #if str($avg_size)
+                --avg-size $avg_size
+            #end if
+            #if str($min_size)
+                --min-size $min_size
+            #end if
+            --output capture.antitarget.bed
+    ]]></command>
+    <inputs>
+        <param name="targets_file" type="data" format="bed" label="input BED or interval file" help="" />
+        <param argument="--access" type="data" optional="true" format="bed" label=" Regions of accessible sequence on chromosomes" help="" />
+        <param argument="--avg-size" optional="true" type="integer" label="Average size of antitarget bins" min="1" value="150000" help="" />
+        <param argument="--min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="25000" help="" />
+    </inputs>
+    <outputs>
+        <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: capture antitarget regions" from_work_dir="capture.antitarget.bed" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="targets_file" ftype="bed" value="capture.bed" />
+            <param name="access" ftype="bed" value="access-excludes.bed" />
+            <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 
+        </test>
+    </tests>
+    <help><![CDATA[
+         Given a “target” BED file that lists the chromosomal coordinates of the tiled
+         regions used for targeted resequencing, derive a BED file off-target/”antitarget” regions.
+    ]]></help>
+    <expand macro="citations" />
+</tool>