Mercurial > repos > mvdbeek > bam_readtagger
comparison bam_readtagger.xml @ 20:03415763c62c draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
author | mvdbeek |
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date | Wed, 19 Apr 2017 16:23:12 -0400 |
parents | 97c1b92dbd28 |
children | 1c91108a80d5 |
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19:97c1b92dbd28 | 20:03415763c62c |
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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 |