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comparison bam2consensus.xml @ 0:d32139014ec3 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author jdv
date Wed, 17 Jul 2019 17:47:45 -0400
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children 2367d00c5182
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-1:000000000000 0:d32139014ec3
1 <tool id="b2b_bam2consensus" name="BAM to consensus" version="0.003">
2
3 <description>Re-call consensus based on BAM mapping</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <!--
9 <requirement type="package" version="0.003">b2b-utils</requirement>
10 -->
11 <requirement type="package" version="7.407">mafft</requirement>
12 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
13 <requirement type="package" version="6.1">ncurses</requirement>
14 <requirement type="package" version="1.9">samtools</requirement>
15 <requirement type="package" version="0.006007">perl-biox-seq</requirement>
16 <requirement type="package" version="1.23">perl-file-which</requirement>
17 </requirements>
18
19 <!-- ***************************************************************** -->
20
21 <version_command>bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command>
22
23 <!-- ***************************************************************** -->
24
25 <command detect_errors="aggressive">
26 <![CDATA[
27
28 ln -s $ref_file ref.tmp;
29 ln -s $in_bam in.bam;
30 samtools faidx ref.tmp;
31 samtools index in.bam;
32
33 bam2consensus
34 --ref ref.tmp
35 --bam in.bam
36 --min_qual $min_qual
37 --min_depth $min_depth
38 --trim $trim
39 --window $window
40 --bg_bin_figs $bg_bin_figs
41 --verbose
42 #if $output_fasta:
43 --consensus $out_fasta
44 #end if
45 #if $output_tsv:
46 --table $out_tsv
47 #end if
48 #if $output_bg:
49 --bedgraph $out_bg
50 #end if
51 ]]>
52 </command>
53
54 <!-- ***************************************************************** -->
55
56 <inputs>
57 <param name="in_bam" type="data" format="bam" label="BAM mapping file to use for consensus calling" help="BAM format" />
58 <param name="ref_file" type="data" format="fasta" label="Reference sequence used for generating BAM" help="FASTA format" />
59 <param argument="min_qual" size="4" type="integer" value="10" min="0" label="Minimum base quality to use for frequency calculations" />
60 <param argument="min_depth" size="4" type="integer" value="3" min="0" label="Minimum consensus depth to call a base (otherwise called as N)" />
61 <param argument="trim" size="4" type="float" value="0.2" min="0" label="Fraction to trim from each end when calculating trimmed mean of error window" />
62 <param argument="window" size="4" type="integer" value="30" min="3" label="Size of sliding window used to calculate local error rates" />
63 <param argument="bg_bin_figs" size="4" type="integer" value="0" min="0" label="Number of sig figs used to bin bedgraph depths (0 = no binning)" />
64 <param name="output_fasta" type="boolean" label="Output FASTA consensus" />
65 <param name="output_tsv" type="boolean" label="Output consensus/frequency table (tab-delim)" />
66 <param name="output_bg" type="boolean" label="Output bedgraph coverage file" />
67 </inputs>
68
69 <!-- ***************************************************************** -->
70
71 <outputs>
72 <data name="out_fasta" format="fasta" label="consensus (FASTA)">
73 <filter>output_fasta is True</filter>
74 </data>
75 <data name="out_tsv" format="tabular" label="frequency table (tab-delim)">
76 <filter>output_tsv is True</filter>
77 </data>
78 <data name="out_bg" format="bedgraph" label="coverage depth (bedgraph)">
79 <filter>output_bg is True</filter>
80 </data>
81 </outputs>
82
83 <!-- ***************************************************************** -->
84
85 <tests>
86 <test>
87 <param name="in_bam" value="b2c.bam" ftype="bam" />
88 <param name="ref_file" value="b2c.mod.fa" ftype="fasta" />
89 <param name="min_qual" value="8" />
90 <param name="min_depth" value="3" />
91 <param name="bg_bin_figs" value="1" />
92 <param name="output_fasta" value="True" />
93 <param name="output_tsv" value="True" />
94 <param name="output_bg" value="True" />
95 <output name="out_fasta" file="b2c.out.fa" compare="diff" />
96 <output name="out_tsv" file="b2c.out.tsv" compare="diff" />
97 <output name="out_bg" file="b2c.out.bg" compare="diff" />
98 </test>
99 </tests>
100
101 <!-- ***************************************************************** -->
102
103 <help>
104
105 bam2consensus is a utility from b2b-utils for calling a new consensus
106 sequence (and producing associated coverage depth and tabular outputs)
107 based on raw read mapping to a genome assembly.
108
109 </help>
110
111 <!-- ***************************************************************** -->
112
113 <citations>
114 </citations>
115
116 </tool>