Mercurial > repos > jdv > b2b_bam2consensus

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