Mercurial > repos > mvdbeek > bam_readtagger

annotate bam_readtagger.xml @ 2:39d9bc17ec74 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit b0627386ac1cc004dc71fc788bf37111213b1fab-dirty
author mvdbeek
date Fri, 17 Feb 2017 12:55:58 -0500
parents f69131f584e8
children cb9036583afe
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.1.13">
0
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2 <description>from multiple bam files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.1.13">readtagger</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 readtagger -t '$tag_file' -a
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11 #for $element in $alignment_series
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12 '$element.annotate_with':$element.r_tag:$element.m_tag
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13 #end for
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14 $allow_dovetailing
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15 $keep_suboptimal
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16 $discarded
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17 $verified
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18 -o '$tagged_file'
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19 ]]></command>
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20 <inputs>
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21 <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
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22 <repeat name="alignment_series" title="Alignments">
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23 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
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24 <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
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25 <expand macro="tag_options"/>
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26 </param>
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27 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
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28 <expand macro="tag_options"/>
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29 </param>
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30 </repeat>
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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"/>
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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"/>
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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"/>
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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"/>
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35 </inputs>
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36 <outputs>
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37 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
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38 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
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39 <filter>verified is True</filter>
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40 </data>
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41 <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string">
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42 <filter>verified is True</filter>
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43 </data>
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44 </outputs>
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45 <tests>
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46 <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) -->
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47 <param name="tag_file" value="dm6.bam" ftype="bam"/>
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48 <repeat name="alignment_series">
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49 <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/>
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50 <param name="r_tag" value="A"/>
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51 <param name="m_tag" value="B"/>
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52 </repeat>
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53 <param name="discarded" value="True"/>
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54 <param name="verified" value="True"/>
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55 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
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56 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
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57 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
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58 </test>
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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) -->
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60 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
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61 <repeat name="alignment_series">
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62 <param name="annotate_with" value="dm6.bam" ftype="bam"/>
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63 <param name="r_tag" value="A"/>
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64 <param name="m_tag" value="B"/>
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65 </repeat>
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66 <param name="discarded" value="True"/>
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67 <param name="verified" value="True"/>
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68 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
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69 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
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70 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
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75 OUTPUT_FILE
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76
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77 Tag reads in an alignment file based on other alignment files
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78
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79 optional arguments:
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80 -h, --help show this help message and exit
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81 -t TAG_FILE, --tag_file TAG_FILE
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82 Tag reads in this file. (default: None)
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83 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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84 Tag reads in readfile if reads are aligned in these
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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85 files.Append `:A:B` to tag first letter of tag
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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86 describing read as A, and first letter of tag
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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87 describing the mate as B (default: None)
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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88 -o OUTPUT_FILE, --output_file OUTPUT_FILE
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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89 Write bam file to this path (default: None)
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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90
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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91 ]]></help>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
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92 </tool>