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comparison target.xml @ 0:f2e5acaf0c0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author iuc
date Sun, 14 May 2023 20:03:48 +0000
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children 93e7e60dba0b
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-1:000000000000 0:f2e5acaf0c0c
1 <tool id="cnvkit_target" name="CNVkit Target" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Prepare a BED file of baited regions for use with CNVkit</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' ./capture.bed &&
10 #if $annotate
11 ln -s '$annotate' ./annotate.bed &&
12 #end if
13 cnvkit.py target
14 '$input_file'
15 --output capture.split.bed
16 #if $annotate
17 --annotate ./annotate.bed
18 #end if
19 $short_names
20 $split
21 #if str($avg_size)
22 --avg-size $avg_size
23 #end if
24 ]]></command>
25 <inputs>
26 <param name="input_file" type="data" format="bed" label="Input BED file" help="" />
27 <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file, BED, interval list, GFF, or similar" />
28 <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels to be short and consistent" help="" />
29 <param argument="--split" type="boolean" checked="false" truevalue="--split" falsevalue="" label="Split large tiled intervals into smaller, consecutive targets" help="" />
30 <param argument="--avg-size" type="integer" optional="true" label="Average size of split target bins" min ="1" value="266" help="" />
31 </inputs>
32 <outputs>
33 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: capture split" from_work_dir="capture.split.bed" />
34 </outputs>
35 <tests>
36 <test expect_num_outputs="1">
37 <param name="input_file" ftype="bed" value="capture.bed" />
38 <param name="split" value="1" />
39 <param name="short_names" value="1" />
40 <output name="out_capture_target">
41 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
42 </output>
43 </test>
44 </tests>
45 <help><![CDATA[
46 Transform bait intervals into targets more suitable for CNVkit.
47 ]]></help>
48 <expand macro="citations" />
49 </tool>