Mercurial > repos > iuc > cnvkit_antitarget

annotate antitarget.xml @ 4:b888e0baaa49 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 11:52:06 +0000
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d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_antitarget" name="CNVkit Antitarget" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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b888e0baaa49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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2 <description>Lists the chromosomal coordinates for targeted resequencing</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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6 <expand macro="xrefs"/>
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d3e992eca99a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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7 <expand macro="creators"/>
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d0f5f5d4262a 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[
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 ln -s '$targets_file' ./capture.bed &&
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #if $access
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 ln -s '$access' ./access.bed &&
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #end if
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 cnvkit.py antitarget
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 ./capture.bed
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 #if $access
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 --access ./access.bed
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 #end if
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 #if str($avg_size)
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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20 --avg-size $avg_size
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 #end if
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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22 #if str($min_size)
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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23 --min-size $min_size
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 #end if
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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25 --output capture.antitarget.bed
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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26 ]]></command>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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27 <inputs>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 <param name="targets_file" type="data" format="bed" label="input BED or interval file" help="" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 <param argument="--access" type="data" optional="true" format="bed" label=" Regions of accessible sequence on chromosomes" help="" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 <param argument="--avg-size" optional="true" type="integer" label="Average size of antitarget bins" min="1" value="150000" help="" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 <param argument="--min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="25000" help="" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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32 </inputs>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 <outputs>
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34 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: capture antitarget regions" from_work_dir="capture.antitarget.bed" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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35 </outputs>
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36 <tests>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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37 <test expect_num_outputs="1">
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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38 <param name="targets_file" ftype="bed" value="capture.bed" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 <param name="access" ftype="bed" value="access-excludes.bed" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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41 </test>
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42 </tests>
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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43 <help><![CDATA[
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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44 Given a “target” BED file that lists the chromosomal coordinates of the tiled
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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45 regions used for targeted resequencing, derive a BED file off-target/”antitarget” regions.
d0f5f5d4262a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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46 ]]></help>
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47 <expand macro="citations" />
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48 </tool>