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comparison bam_readtagger.xml @ 3:cb9036583afe draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
author mvdbeek
date Tue, 21 Feb 2017 04:39:31 -0500
parents 39d9bc17ec74
children 7625c594bc37
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2:39d9bc17ec74 3:cb9036583afe
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.1.13"> 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.2.0">
2 <description>from multiple bam files</description> 2 <description>from multiple bam files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.1.13">readtagger</requirement> 7 <requirement type="package" version="0.2.0">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 readtagger -t '$tag_file' -a 10 readtagger -t '$tag_file' -a
11 #for $element in $alignment_series 11 #for $element in $alignment_series
12 '$element.annotate_with':$element.r_tag:$element.m_tag 12 '$element.annotate_with':$element.r_tag:$element.m_tag
13 #end for 13 #end for
14 $allow_dovetailing 14 $allow_dovetailing
15 $keep_suboptimal 15 $keep_suboptimal
16 $discarded 16 $discarded
17 $verified 17 $verified
18 $discard_proper_pairs
18 -o '$tagged_file' 19 -o '$tagged_file'
19 ]]></command> 20 ]]></command>
20 <inputs> 21 <inputs>
21 <param name="tag_file" argument="--tag_file" type="data" format="bam"/> 22 <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
22 <repeat name="alignment_series" title="Alignments"> 23 <repeat name="alignment_series" title="Alignments">
28 <expand macro="tag_options"/> 29 <expand macro="tag_options"/>
29 </param> 30 </param>
30 </repeat> 31 </repeat>
31 <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/> 32 <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
32 <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/> 33 <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/>
34 <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/>
33 <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/> 35 <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
34 <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/> 36 <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
35 </inputs> 37 </inputs>
36 <outputs> 38 <outputs>
37 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/> 39 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
67 <param name="verified" value="True"/> 69 <param name="verified" value="True"/>
68 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" /> 70 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
69 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/> 71 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
70 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/> 72 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
71 </test> 73 </test>
74 <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
75 <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
76 <repeat name="alignment_series">
77 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>
78 <param name="r_tag" value="A"/>
79 <param name="m_tag" value="B"/>
80 </repeat>
81 <param name="discarded" value="True"/>
82 <param name="keep_suboptimal" value="True"/>
83 <param name="discard_proper_pairs" value="True"/>
84 <param name="verified" value="True"/>
85 <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" />
86 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/>
87 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/>
88 </test>
72 </tests> 89 </tests>
73 <help><![CDATA[ 90 <help><![CDATA[
74 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o 91 .. code-block::
75 OUTPUT_FILE
76 92
77 Tag reads in an alignment file based on other alignment files 93 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
94 OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED]
95 [-wv WRITE_VERIFIED] [--version]
78 96
79 optional arguments: 97 Tag reads in an alignment file based on other alignment files
80 -h, --help show this help message and exit 98
81 -t TAG_FILE, --tag_file TAG_FILE 99 optional arguments:
82 Tag reads in this file. (default: None) 100 -h, --help show this help message and exit
83 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] 101 -t TAG_FILE, --tag_file TAG_FILE
84 Tag reads in readfile if reads are aligned in these 102 Tag reads in this file. (default: None)
85 files.Append `:A:B` to tag first letter of tag 103 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
86 describing read as A, and first letter of tag 104 Tag reads in readfile if reads are aligned in these
87 describing the mate as B (default: None) 105 files.Append `:A:B` to tag first letter of tag
88 -o OUTPUT_FILE, --output_file OUTPUT_FILE 106 describing read as A, and first letter of tag
89 Write bam file to this path (default: None) 107 describing the mate as B (default: None)
108 -o OUTPUT_FILE, --output_file OUTPUT_FILE
109 Write bam file to this path (default: None)
110 -d, --allow_dovetailing
111 Sets the proper pair flag (0x0002) to true if reads
112 dovetail [reads reach into or surpass the mate
113 sequence]. (default: False)
114 -dp, --discard_if_proper_pair
115 Discard an alternative flag if the current read is in
116 a proper pair. (default: False)
117 -k, --keep_suboptimal_alternate_tags
118 By default cigarstrings of the alternative tags are
119 compared and alternates that are not explaining the
120 current cigar strings are discarded. Use this option
121 to keep the alternative tags (effectively restoring
122 the behaviour of readtagger < 0.1.4) (default: False)
123 -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED
124 Write discarded reads into separate file (default:
125 False)
126 -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED
127 Write verified reads into separate file (default:
128 False)
129 --version show program's version number and exit
90 130
91 ]]></help> 131 ]]></help>
92 </tool> 132 </tool>