Mercurial > repos > mvdbeek > bam_readtagger

annotate bam_readtagger.xml @ 73:676b7ff2d899 draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfb6ee6e3587f19540eb97d9b761623728aa6ee8"
author mvdbeek
date Sat, 11 Jan 2020 16:20:59 -0500
parents 8ef26717ba8b
children 6c15dd4415ea
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73
676b7ff2d899 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfb6ee6e3587f19540eb97d9b761623728aa6ee8"
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.5.20">
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2 <description>from multiple bam files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.5.20">readtagger</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 readtagger -t '$tag_file' -s
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11 #for $element in $alignment_series
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12 '$element.annotate_with':$element.r_tag:$element.m_tag
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13 #end for
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14 #if $reference_fasta:
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15 --reference_fasta '$reference_fasta'
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16 #end if
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17 $allow_dovetailing
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18 $discard_suboptimal
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19 $discarded
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20 $verified
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21 $discard_proper_pairs
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22 --cores "\${GALAXY_SLOTS:-2}"
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23 -o '$tagged_file'
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24 ]]></command>
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25 <inputs>
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26 <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_sorted.bam"/>
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27 <repeat name="alignment_series" title="Alignments">
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28 <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_sorted.bam"/>
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29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
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30 <expand macro="tag_options"/>
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31 </param>
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32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
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33 <expand macro="tag_options"/>
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34 </param>
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35 </repeat>
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36 <param argument="--reference_fasta" type="data" format="fasta" label="Reference fasta for realigning clipped reads" optional="True" help="This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file."/>
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37 <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
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38 <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/>
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39 <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/>
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40 <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
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41 <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
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42 </inputs>
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43 <outputs>
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44 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
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45 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
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46 <filter>verified is True</filter>
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47 </data>
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48 <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string">
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49 <filter>verified is True</filter>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) -->
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54 <param name="tag_file" value="dm6.bam" ftype="bam"/>
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55 <repeat name="alignment_series">
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56 <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/>
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57 <param name="r_tag" value="A"/>
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58 <param name="m_tag" value="B"/>
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59 </repeat>
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60 <param name="discarded" value="True"/>
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61 <param name="verified" value="True"/>
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62 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
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63 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
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64 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
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65 </test>
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66 <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
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67 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
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68 <repeat name="alignment_series">
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69 <param name="annotate_with" value="dm6.bam" ftype="bam"/>
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70 <param name="r_tag" value="A"/>
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71 <param name="m_tag" value="B"/>
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72 </repeat>
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73 <param name="discarded" value="True"/>
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74 <param name="verified" value="True"/>
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75 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" />
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76 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/>
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77 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/>
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78 </test>
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79 <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
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80 <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
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81 <repeat name="alignment_series">
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82 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>
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83 <param name="r_tag" value="A"/>
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84 <param name="m_tag" value="B"/>
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85 </repeat>
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86 <param name="discarded" value="True"/>
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87 <param name="keep_suboptimal" value="True"/>
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88 <param name="discard_proper_pairs" value="True"/>
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89 <param name="verified" value="True"/>
20
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90 <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
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91 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
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92 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
3
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93 </test>
0
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94 </tests>
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95 <help><![CDATA[
3
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96 .. code-block::
0
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97
3
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98 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
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99 OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED]
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100 [-wv WRITE_VERIFIED] [--version]
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101
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102 Tag reads in an alignment file based on other alignment files
0
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103
3
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104 optional arguments:
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105 -h, --help show this help message and exit
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106 -t TAG_FILE, --tag_file TAG_FILE
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107 Tag reads in this file. (default: None)
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108 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
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109 Tag reads in readfile if reads are aligned in these
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110 files.Append `:A:B` to tag first letter of tag
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111 describing read as A, and first letter of tag
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112 describing the mate as B (default: None)
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113 -o OUTPUT_FILE, --output_file OUTPUT_FILE
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114 Write bam file to this path (default: None)
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115 -d, --allow_dovetailing
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116 Sets the proper pair flag (0x0002) to true if reads
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117 dovetail [reads reach into or surpass the mate
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118 sequence]. (default: False)
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119 -dp, --discard_if_proper_pair
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120 Discard an alternative flag if the current read is in
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121 a proper pair. (default: False)
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122 -k, --keep_suboptimal_alternate_tags
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123 By default cigarstrings of the alternative tags are
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124 compared and alternates that are not explaining the
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125 current cigar strings are discarded. Use this option
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126 to keep the alternative tags (effectively restoring
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127 the behaviour of readtagger < 0.1.4) (default: False)
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128 -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED
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129 Write discarded reads into separate file (default:
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130 False)
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131 -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED
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132 Write verified reads into separate file (default:
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133 False)
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134 --version show program's version number and exit
0
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135
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136 ]]></help>
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137 </tool>