Mercurial > repos > iuc > cnvkit_target

annotate target.xml @ 4:a5e835897cbd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:56:53 +0000
parents 93e7e60dba0b
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f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_target" name="CNVkit Target" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Prepare a BED file of baited regions for use with CNVkit</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="creators"/>
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f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 ln -s '$input_file' ./capture.bed &&
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #if $annotate
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12 ln -s '$annotate' ./annotate.bed &&
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #end if
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 cnvkit.py target
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 '$input_file'
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16 --output capture.split.bed
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17 #if $annotate
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18 --annotate ./annotate.bed
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19 #end if
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20 $short_names
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21 $split
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22 #if str($avg_size)
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23 --avg-size $avg_size
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24 #end if
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25 ]]></command>
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26 <inputs>
1
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27 <param name="input_file" type="data" format="bed" label="capture/target BED file" help="" />
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f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 <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" />
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels to be short and consistent" help="" />
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 <param argument="--split" type="boolean" checked="false" truevalue="--split" falsevalue="" label="Split large tiled intervals into smaller, consecutive targets" help="" />
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 <param argument="--avg-size" type="integer" optional="true" label="Average size of split target bins" min ="1" value="266" help="" />
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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32 </inputs>
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33 <outputs>
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34 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: capture split" from_work_dir="capture.split.bed" />
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35 </outputs>
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36 <tests>
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37 <test expect_num_outputs="1">
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38 <param name="input_file" ftype="bed" value="capture.bed" />
f2e5acaf0c0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 <param name="split" value="1" />
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40 <param name="short_names" value="1" />
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41 <output name="out_capture_target">
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42 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 Transform bait intervals into targets more suitable for CNVkit.
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>