diff target.xml @ 0:0350116f0c25 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/target.xml	Sun May 14 20:08:09 2023 +0000
@@ -0,0 +1,49 @@
+<tool id="cnvkit_target" name="CNVkit Target" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Prepare a BED file of baited regions for use with CNVkit</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+    ln -s '$input_file' ./capture.bed &&
+    #if $annotate
+        ln -s '$annotate' ./annotate.bed &&
+    #end if
+    cnvkit.py target
+        '$input_file'
+        --output capture.split.bed
+        #if $annotate
+            --annotate ./annotate.bed
+        #end if
+        $short_names
+        $split
+        #if str($avg_size)
+             --avg-size $avg_size
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="bed" label="Input BED file" help="" />
+        <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file, BED, interval list, GFF, or similar" />
+        <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels to be short and consistent" help="" />
+        <param argument="--split" type="boolean" checked="false" truevalue="--split" falsevalue="" label="Split large tiled intervals into smaller, consecutive targets" help="" />
+        <param argument="--avg-size" type="integer" optional="true" label="Average size of split target bins" min ="1" value="266" help="" />
+    </inputs>
+    <outputs>
+        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: capture split" from_work_dir="capture.split.bed" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_file" ftype="bed" value="capture.bed" />
+            <param name="split" value="1" />
+            <param name="short_names" value="1" />
+            <output name="out_capture_target">
+                <assert_contents><has_text_matching expression="chrM"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+             Transform bait intervals into targets more suitable for CNVkit.
+    ]]></help>
+    <expand macro="citations" />
+</tool>