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comparison autobin.xml @ 0:b1f6ea16e629 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 20:05:09 +0000
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children 96941b733d87
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-1:000000000000 0:b1f6ea16e629
1 <tool id="cnvkit_autobin" name="CNVkit Autobin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Estimates read counts or depths in a BAM file</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 #import re
10 #set $names = []
11 #set $x=1
12 #for $x, $bam in enumerate($bams):
13 #set $name_base = re.sub('[^\w\-_\.]', '_', $bam.element_identifier)
14 #set $name = $name_base + '_' + str(x)
15 #silent $names.append( $name )
16 ln -s '$bam' ${name}.bam &&
17 ln -s '${bam.metadata.bam_index}' ${name}.bai &&
18 #end for
19 ln -s '$targets' ./capture.bed &&
20 #if $advanced_settings.reference_source.fasta
21 #if str($advanced_settings.reference_source.ref_selector) == 'history':
22 ln -s '$advanced_settings.reference_source.fasta' ./genome.fa &&
23 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
24 #else
25 ln -s '$advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
26 ln -s '${advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
27 #end if
28 #end if
29 #if $advanced_settings.access
30 ln -s '$advanced_settings.access' ./access.bed &&
31 #end if
32 #if $advanced_settings.annotate
33 ln -s '$advanced_settings.annotate' ./annotate.bed &&
34 #end if
35 #if $advanced_settings.target_output_bed
36 ln -s '$advanced_settings.target_output_bed' ./target_output.bed &&
37 #end if
38 #if $advanced_settings.antitarget_output_bed
39 ln -s '$advanced_settings.antitarget_output_bed' ./antitarget_output.bed &&
40 #end if
41 cnvkit.py autobin
42 #for $name in $names:
43 ${name}.bam
44 #end for
45 --targets ./capture.bed
46 #if $advanced_settings.method == "hybrid"
47 #set $method_val = "hybrid"
48 --method '$method_val'
49 #else
50 --method '$method'
51 #end if
52 #if $advanced_settings.access
53 --access ./access.bed
54 #end if
55 #if str($advanced_settings.bp_per_bin)
56 --bp-per-bin $advanced_settings.bp_per_bin
57 #end if
58 #if str($advanced_settings.target_max_size)
59 --target-max-size $advanced_settings.target_max_size
60 #end if
61 #if str($advanced_settings.target_min_size)
62 --target-min-size $advanced_settings.target_min_size
63 #end if
64 #if str($advanced_settings.antitarget_max_size)
65 --antitarget-max-size $advanced_settings.antitarget_max_size
66 #end if
67 #if str($advanced_settings.antitarget_min_size)
68 --antitarget-min-size $advanced_settings.antitarget_min_size
69 #end if
70 #if $advanced_settings.annotate
71 --annotate ./annotate.bed
72 #end if
73 $advanced_settings.short_names
74 #if $advanced_settings.target_output_bed
75 --target-output-bed ./target_output.bed
76 #end if
77 #if $advanced_settings.antitarget_output_bed
78 --antitarget-output-bed ./antitarget_output.bed
79 #end if
80 ]]></command>
81 <inputs>
82 <param name="bams" type="data" multiple="true" format="bam" label="Input Sample BAM file/s" help="" />
83 <param argument="--targets" type="data" format="bed,tabular" label="Input Potentially targeted genomic regions" help="e.g. all possible exons for the reference genome. Format: BED, interval list, etc." />
84 <section name="advanced_settings" title="Advanced settings" expanded="false">
85 <expand macro="reference_interface" />
86 <expand macro="autobin_optional" />
87 </section>
88 </inputs>
89 <outputs>
90 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture target" from_work_dir="capture.target.bed" />
91 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture antitarget" from_work_dir="capture.antitarget.bed" />
92 </outputs>
93 <tests>
94 <test expect_num_outputs="2">
95 <conditional name="reference_source">
96 <param name="ref_selector" value="history"/>
97 <param name="fasta" ftype="fasta" value="genome.fasta" />
98 </conditional>
99 <param name="bams" ftype="bam" value="tumor.bam" />
100 <param name="targets" ftype="bed" value="capture.bed" />
101 <output name="out_capture_target" file="capture.target.bed" />
102 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
103 </test>
104 <test expect_num_outputs="2">
105 <conditional name="reference_source">
106 <param name="ref_selector" value="cached"/>
107 <param name="fasta" value="test_buildid"/>
108 </conditional>
109 <param name="bams" ftype="bam" value="tumor.bam" />
110 <param name="targets" ftype="bed" value="capture.bed" />
111 <output name="out_capture_target" file="capture.target.bed" />
112 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
113 </test>
114 <test expect_num_outputs="2">
115 <param name="bams" ftype="bam" value="tumor.bam,tumor_1.bam" />
116 <param name="targets" ftype="bed" value="capture.bed" />
117 <output name="out_capture_target" file="capture.target.bed" />
118 <output name="out_capture_antitarget" file="multible_capture.antitarget.bed" />
119 </test>
120 </tests>
121 <help><![CDATA[
122 Quickly estimate read counts or depths in a BAM file to estimate reasonable on- and (if relevant) off-target bin sizes.
123 ]]></help>
124 <expand macro="citations" />
125 </tool>