Mercurial > repos > mvdbeek > bam_readtagger

comparison bam_readtagger.xml @ 21:4dd759a1372c draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450
author mvdbeek
date Wed, 19 Apr 2017 16:22:58 -0400
parents 44bbb5c4553f
children 32e191f572e1
comparison
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20:44bbb5c4553f 21:4dd759a1372c
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.13"> 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.14">
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="0.3.13">readtagger</requirement> 7 <requirement type="package" version="0.3.14">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
52 <param name="r_tag" value="A"/> 52 <param name="r_tag" value="A"/>
53 <param name="m_tag" value="B"/> 53 <param name="m_tag" value="B"/>
54 </repeat> 54 </repeat>
55 <param name="discarded" value="True"/> 55 <param name="discarded" value="True"/>
56 <param name="verified" value="True"/> 56 <param name="verified" value="True"/>
57 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/> 57 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
58 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/> 58 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
59 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/> 59 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
60 </test> 60 </test>
61 <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) --> 61 <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) -->
62 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/> 62 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
63 <repeat name="alignment_series"> 63 <repeat name="alignment_series">
64 <param name="annotate_with" value="dm6.bam" ftype="bam"/> 64 <param name="annotate_with" value="dm6.bam" ftype="bam"/>
65 <param name="r_tag" value="A"/> 65 <param name="r_tag" value="A"/>
66 <param name="m_tag" value="B"/> 66 <param name="m_tag" value="B"/>
67 </repeat> 67 </repeat>
68 <param name="discarded" value="True"/> 68 <param name="discarded" value="True"/>
69 <param name="verified" value="True"/> 69 <param name="verified" value="True"/>
70 <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="7" />
71 <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="7"/>
72 <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="7"/>
73 </test> 73 </test>
74 <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair --> 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"/> 75 <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
76 <repeat name="alignment_series"> 76 <repeat name="alignment_series">
77 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/> 77 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>
80 </repeat> 80 </repeat>
81 <param name="discarded" value="True"/> 81 <param name="discarded" value="True"/>
82 <param name="keep_suboptimal" value="True"/> 82 <param name="keep_suboptimal" value="True"/>
83 <param name="discard_proper_pairs" value="True"/> 83 <param name="discard_proper_pairs" value="True"/>
84 <param name="verified" 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" /> 85 <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
86 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/> 86 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
87 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/> 87 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
88 </test> 88 </test>
89 </tests> 89 </tests>
90 <help><![CDATA[ 90 <help><![CDATA[
91 .. code-block:: 91 .. code-block::
92 92