Mercurial > repos > mvdbeek > bam_readtagger

annotate bam_readtagger.xml @ 38:f6311a04a6c9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
author mvdbeek
date Thu, 15 Mar 2018 05:13:22 -0400
parents 93f7962a3e19
children 4b1ebfcd0f46
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents: 37
diff changeset
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.9">
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
2 <description>from multiple bam files</description>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
3 <macros>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
4 <import>macros.xml</import>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
5 </macros>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
6 <requirements>
38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents: 37
diff changeset
7 <requirement type="package" version="0.4.9">readtagger</requirement>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
8 </requirements>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
28
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
10 readtagger -t '$tag_file' -s
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
11 #for $element in $alignment_series
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
12 '$element.annotate_with':$element.r_tag:$element.m_tag
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
13 #end for
29
2c62ca47c455 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
mvdbeek
parents: 28
diff changeset
14 #if $reference_fasta:
2c62ca47c455 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
mvdbeek
parents: 28
diff changeset
15 --reference_fasta '$reference_fasta'
2c62ca47c455 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
mvdbeek
parents: 28
diff changeset
16 #end if
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
17 $allow_dovetailing
28
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
18 $discard_suboptimal
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
19 $discarded
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
20 $verified
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
21 $discard_proper_pairs
22
42fefb316c95 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12-dirty
mvdbeek
parents: 21
diff changeset
22 --cores "\${GALAXY_SLOTS:-2}"
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
23 -o '$tagged_file'
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
24 ]]></command>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
25 <inputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
26 <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
27 <repeat name="alignment_series" title="Alignments">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
28 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
30 <expand macro="tag_options"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
31 </param>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
33 <expand macro="tag_options"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
34 </param>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
35 </repeat>
29
2c62ca47c455 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
mvdbeek
parents: 28
diff changeset
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."/>
28
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
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"/>
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
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"/>
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
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"/>
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
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"/>
be95c9c82937 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
mvdbeek
parents: 27
diff changeset
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"/>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
42 </inputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
43 <outputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
44 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
45 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
46 <filter>verified is True</filter>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
47 </data>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
48 <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
49 <filter>verified is True</filter>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
50 </data>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
51 </outputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
52 <tests>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
53 <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) -->
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
54 <param name="tag_file" value="dm6.bam" ftype="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
55 <repeat name="alignment_series">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
56 <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
57 <param name="r_tag" value="A"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
58 <param name="m_tag" value="B"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
59 </repeat>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
60 <param name="discarded" value="True"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
61 <param name="verified" value="True"/>
20
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
62 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
63 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
64 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
65 </test>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
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) -->
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
67 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
68 <repeat name="alignment_series">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
69 <param name="annotate_with" value="dm6.bam" ftype="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
70 <param name="r_tag" value="A"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
71 <param name="m_tag" value="B"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
72 </repeat>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
73 <param name="discarded" value="True"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
74 <param name="verified" value="True"/>
20
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
75 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" />
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
76 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/>
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
77 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
78 </test>
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
79 <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
80 <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
81 <repeat name="alignment_series">
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
82 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
83 <param name="r_tag" value="A"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
84 <param name="m_tag" value="B"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
85 </repeat>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
86 <param name="discarded" value="True"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
87 <param name="keep_suboptimal" value="True"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
88 <param name="discard_proper_pairs" value="True"/>
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
89 <param name="verified" value="True"/>
20
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
90 <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
91 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
03415763c62c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
mvdbeek
parents: 19
diff changeset
92 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
93 </test>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
94 </tests>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
95 <help><![CDATA[
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
96 .. code-block::
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
97
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
98 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
99 OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED]
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
100 [-wv WRITE_VERIFIED] [--version]
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
101
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
102 Tag reads in an alignment file based on other alignment files
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
103
3
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
104 optional arguments:
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
105 -h, --help show this help message and exit
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
106 -t TAG_FILE, --tag_file TAG_FILE
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
107 Tag reads in this file. (default: None)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
108 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
109 Tag reads in readfile if reads are aligned in these
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
110 files.Append `:A:B` to tag first letter of tag
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
111 describing read as A, and first letter of tag
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
112 describing the mate as B (default: None)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
113 -o OUTPUT_FILE, --output_file OUTPUT_FILE
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
114 Write bam file to this path (default: None)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
115 -d, --allow_dovetailing
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
116 Sets the proper pair flag (0x0002) to true if reads
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
117 dovetail [reads reach into or surpass the mate
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
118 sequence]. (default: False)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
119 -dp, --discard_if_proper_pair
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
120 Discard an alternative flag if the current read is in
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
121 a proper pair. (default: False)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
122 -k, --keep_suboptimal_alternate_tags
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
123 By default cigarstrings of the alternative tags are
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
124 compared and alternates that are not explaining the
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
125 current cigar strings are discarded. Use this option
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
126 to keep the alternative tags (effectively restoring
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
127 the behaviour of readtagger < 0.1.4) (default: False)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
128 -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
129 Write discarded reads into separate file (default:
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
130 False)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
131 -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
132 Write verified reads into separate file (default:
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
133 False)
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
diff changeset
134 --version show program's version number and exit
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
135
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
136 ]]></help>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
137 </tool>