Mercurial > repos > mvdbeek > bam_readtagger
annotate bam_readtagger.xml @ 42:5b8781514bc1 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
author | mvdbeek |
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date | Thu, 24 May 2018 11:51:27 -0400 |
parents | 4fdf606153df |
children | 6f9b1b81b593 |
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41
4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.11"> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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2 <description>from multiple bam files</description> |
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3 <macros> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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4 <import>macros.xml</import> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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5 </macros> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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6 <requirements> |
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4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
mvdbeek
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7 <requirement type="package" version="0.4.11">readtagger</requirement> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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8 </requirements> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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9 <command detect_errors="aggressive"><![CDATA[ |
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10 readtagger -t '$tag_file' -s |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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11 #for $element in $alignment_series |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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12 '$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
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13 #end for |
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14 #if $reference_fasta: |
2c62ca47c455
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
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15 --reference_fasta '$reference_fasta' |
2c62ca47c455
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
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16 #end if |
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a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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17 $allow_dovetailing |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
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18 $discard_suboptimal |
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a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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19 $discarded |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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20 $verified |
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21 $discard_proper_pairs |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12-dirty
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22 --cores "\${GALAXY_SLOTS:-2}" |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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23 -o '$tagged_file' |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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24 ]]></command> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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25 <inputs> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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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
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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
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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
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30 <expand macro="tag_options"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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31 </param> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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33 <expand macro="tag_options"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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34 </param> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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35 </repeat> |
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2c62ca47c455
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty
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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."/> |
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be95c9c82937
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty
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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
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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
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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
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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
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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"/> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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42 </inputs> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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43 <outputs> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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45 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string"> |
a38447a59412
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46 <filter>verified is True</filter> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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47 </data> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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49 <filter>verified is True</filter> |
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50 </data> |
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51 </outputs> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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52 <tests> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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53 <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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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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55 <repeat name="alignment_series"> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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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
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57 <param name="r_tag" value="A"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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58 <param name="m_tag" value="B"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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59 </repeat> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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60 <param name="discarded" value="True"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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61 <param name="verified" value="True"/> |
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62 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
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63 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/> |
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64 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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65 </test> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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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
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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
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68 <repeat name="alignment_series"> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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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
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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
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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
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72 </repeat> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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73 <param name="discarded" value="True"/> |
a38447a59412
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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74 <param name="verified" value="True"/> |
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75 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" /> |
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76 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/> |
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77 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/> |
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78 </test> |
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79 <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair --> |
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80 <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/> |
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81 <repeat name="alignment_series"> |
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82 <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/> |
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83 <param name="r_tag" value="A"/> |
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84 <param name="m_tag" value="B"/> |
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85 </repeat> |
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86 <param name="discarded" value="True"/> |
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87 <param name="keep_suboptimal" value="True"/> |
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88 <param name="discard_proper_pairs" value="True"/> |
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89 <param name="verified" value="True"/> |
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90 <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" /> |
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91 <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/> |
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92 <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/> |
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93 </test> |
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94 </tests> |
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95 <help><![CDATA[ |
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96 .. code-block:: |
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97 |
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98 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o |
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99 OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED] |
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100 [-wv WRITE_VERIFIED] [--version] |
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101 |
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102 Tag reads in an alignment file based on other alignment files |
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103 |
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104 optional arguments: |
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105 -h, --help show this help message and exit |
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106 -t TAG_FILE, --tag_file TAG_FILE |
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107 Tag reads in this file. (default: None) |
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108 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] |
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109 Tag reads in readfile if reads are aligned in these |
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110 files.Append `:A:B` to tag first letter of tag |
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111 describing read as A, and first letter of tag |
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112 describing the mate as B (default: None) |
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113 -o OUTPUT_FILE, --output_file OUTPUT_FILE |
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114 Write bam file to this path (default: None) |
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115 -d, --allow_dovetailing |
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116 Sets the proper pair flag (0x0002) to true if reads |
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117 dovetail [reads reach into or surpass the mate |
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118 sequence]. (default: False) |
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119 -dp, --discard_if_proper_pair |
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120 Discard an alternative flag if the current read is in |
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121 a proper pair. (default: False) |
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122 -k, --keep_suboptimal_alternate_tags |
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123 By default cigarstrings of the alternative tags are |
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124 compared and alternates that are not explaining the |
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125 current cigar strings are discarded. Use this option |
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126 to keep the alternative tags (effectively restoring |
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127 the behaviour of readtagger < 0.1.4) (default: False) |
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128 -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED |
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129 Write discarded reads into separate file (default: |
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130 False) |
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131 -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED |
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132 Write verified reads into separate file (default: |
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133 False) |
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134 --version show program's version number and exit |
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135 |
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136 ]]></help> |
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137 </tool> |