Mercurial > repos > iuc > cnvkit_autobin

annotate autobin.xml @ 4:4706c14fac55 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 11:50:04 +0000
parents bec5ce50f98f
children
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b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_autobin" name="CNVkit Autobin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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2 <description>Estimates read counts or depths in a BAM file</description>
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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3 <macros>
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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4 <import>macros.xml</import>
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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5 </macros>
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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6 <expand macro="xrefs"/>
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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7 <expand macro="requirements"/>
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96941b733d87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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8 <expand macro="creators"/>
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b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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9 <command detect_errors="exit_code"><![CDATA[
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 #import re
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #set $names = []
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 #set $x=1
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #for $x, $bam in enumerate($bams):
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 #set $name_base = re.sub('[^\w\-_\.]', '_', $bam.element_identifier)
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96941b733d87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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15 #set $name = $name_base
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b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 #silent $names.append( $name )
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 ln -s '$bam' ${name}.bam &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 ln -s '${bam.metadata.bam_index}' ${name}.bai &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 #end for
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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20 ln -s '$targets' ./capture.bed &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 #if $advanced_settings.reference_source.fasta
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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22 #if str($advanced_settings.reference_source.ref_selector) == 'history':
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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23 ln -s '$advanced_settings.reference_source.fasta' ./genome.fa &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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25 #else
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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26 ln -s '$advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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27 ln -s '${advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 #if $advanced_settings.access
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 ln -s '$advanced_settings.access' ./access.bed &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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32 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 #if $advanced_settings.annotate
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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34 ln -s '$advanced_settings.annotate' ./annotate.bed &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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35 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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36 #if $advanced_settings.target_output_bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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37 ln -s '$advanced_settings.target_output_bed' ./target_output.bed &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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38 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 #if $advanced_settings.antitarget_output_bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 ln -s '$advanced_settings.antitarget_output_bed' ./antitarget_output.bed &&
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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41 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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42 cnvkit.py autobin
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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43 #for $name in $names:
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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44 ${name}.bam
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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45 #end for
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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46 --targets ./capture.bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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47 #if $advanced_settings.method == "hybrid"
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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48 #set $method_val = "hybrid"
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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49 --method '$method_val'
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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50 #else
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51 --method '$method'
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52 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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53 #if $advanced_settings.access
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54 --access ./access.bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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55 #end if
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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56 #if str($advanced_settings.bp_per_bin)
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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57 --bp-per-bin $advanced_settings.bp_per_bin
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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58 #end if
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59 #if str($advanced_settings.target_max_size)
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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60 --target-max-size $advanced_settings.target_max_size
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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61 #end if
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62 #if str($advanced_settings.target_min_size)
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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63 --target-min-size $advanced_settings.target_min_size
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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64 #end if
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65 #if str($advanced_settings.antitarget_max_size)
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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66 --antitarget-max-size $advanced_settings.antitarget_max_size
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67 #end if
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68 #if str($advanced_settings.antitarget_min_size)
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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69 --antitarget-min-size $advanced_settings.antitarget_min_size
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70 #end if
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71 #if $advanced_settings.annotate
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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72 --annotate ./annotate.bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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73 #end if
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74 $advanced_settings.short_names
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75 #if $advanced_settings.target_output_bed
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76 --target-output-bed ./target_output.bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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77 #end if
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78 #if $advanced_settings.antitarget_output_bed
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79 --antitarget-output-bed ./antitarget_output.bed
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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80 #end if
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81 ]]></command>
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82 <inputs>
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83 <param name="bams" type="data" multiple="true" format="bam" label="Input Sample BAM file/s" help="" />
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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84 <param argument="--targets" type="data" format="bed,tabular" label="Input Potentially targeted genomic regions" help="e.g. all possible exons for the reference genome. Format: BED, interval list, etc." />
b1f6ea16e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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85 <section name="advanced_settings" title="Advanced settings" expanded="false">
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86 <expand macro="reference_interface" />
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87 <expand macro="autobin_optional" />
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88 </section>
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89 </inputs>
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90 <outputs>
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91 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture target" from_work_dir="capture.target.bed" />
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92 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture antitarget" from_work_dir="capture.antitarget.bed" />
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93 </outputs>
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94 <tests>
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95 <test expect_num_outputs="2">
2
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96 <section name="advanced_settings">
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97 <conditional name="reference_source">
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98 <param name="ref_selector" value="history"/>
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99 <param name="fasta" ftype="fasta" value="genome.fasta" />
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100 </conditional>
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101 </section>
0
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102 <param name="bams" ftype="bam" value="tumor.bam" />
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103 <param name="targets" ftype="bed" value="capture.bed" />
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104 <output name="out_capture_target" file="capture.target.bed" />
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105 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
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106 </test>
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107 <test expect_num_outputs="2">
2
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108 <section name="advanced_settings">
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109 <conditional name="reference_source">
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110 <param name="ref_selector" value="cached"/>
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111 <param name="fasta" value="test_buildid"/>
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112 </conditional>
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113 </section>
0
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114 <param name="bams" ftype="bam" value="tumor.bam" />
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115 <param name="targets" ftype="bed" value="capture.bed" />
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116 <output name="out_capture_target" file="capture.target.bed" />
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117 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
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118 </test>
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119 <test expect_num_outputs="2">
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120 <param name="bams" ftype="bam" value="tumor.bam,tumor_1.bam" />
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121 <param name="targets" ftype="bed" value="capture.bed" />
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122 <output name="out_capture_target" file="capture.target.bed" />
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123 <output name="out_capture_antitarget" file="multible_capture.antitarget.bed" />
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 Quickly estimate read counts or depths in a BAM file to estimate reasonable on- and (if relevant) off-target bin sizes.
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128 ]]></help>
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129 <expand macro="citations" />
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130 </tool>