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comparison bam_readtagger.xml @ 0:92415330ad3e draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
author mvdbeek
date Fri, 17 Feb 2017 10:53:53 -0500
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.1.8">
2 <description>from multiple bam files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.1.8">readtagger</requirement>
8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[
10 readtagger -t '$tag_file' -a
11 #for $element in $alignment_series
12 '$element.annotate_with':$element.r_tag:$element.m_tag
13 #end for
14 $allow_dovetailing
15 $keep_suboptimal
16 $discarded
17 $verified
18 -o '$tagged_file'
19 ]]></command>
20 <inputs>
21 <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
22 <repeat name="alignment_series" title="Alignments">
23 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
24 <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
25 <expand macro="tag_options"/>
26 </param>
27 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
28 <expand macro="tag_options"/>
29 </param>
30 </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="-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="-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"/>
35 </inputs>
36 <outputs>
37 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
38 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
39 <filter>verified is True</filter>
40 </data>
41 <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string">
42 <filter>verified is True</filter>
43 </data>
44 </outputs>
45 <tests>
46 <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) -->
47 <param name="tag_file" value="dm6.bam" ftype="bam"/>
48 <repeat name="alignment_series">
49 <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/>
50 <param name="r_tag" value="A"/>
51 <param name="m_tag" value="B"/>
52 </repeat>
53 <param name="discarded" value="True"/>
54 <param name="verified" value="True"/>
55 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
56 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
57 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
58 </test>
59 <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) -->
60 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
61 <repeat name="alignment_series">
62 <param name="annotate_with" value="dm6.bam" ftype="bam"/>
63 <param name="r_tag" value="A"/>
64 <param name="m_tag" value="B"/>
65 </repeat>
66 <param name="discarded" value="True"/>
67 <param name="verified" value="True"/>
68 <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"/>
70 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
71 </test>
72 </tests>
73 <help><![CDATA[
74 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
75 OUTPUT_FILE
76
77 Tag reads in an alignment file based on other alignment files
78
79 optional arguments:
80 -h, --help show this help message and exit
81 -t TAG_FILE, --tag_file TAG_FILE
82 Tag reads in this file. (default: None)
83 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
84 Tag reads in readfile if reads are aligned in these
85 files.Append `:A:B` to tag first letter of tag
86 describing read as A, and first letter of tag
87 describing the mate as B (default: None)
88 -o OUTPUT_FILE, --output_file OUTPUT_FILE
89 Write bam file to this path (default: None)
90
91 ]]></help>
92 </tool>