Mercurial > repos > iuc > lofreq_alnqual

annotate lofreq_alnqual.xml @ 4:e0e2fd665102 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author iuc
date Mon, 15 Jun 2020 13:13:27 -0400
parents 606542a18f82
children 09d6e4693887
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e0e2fd665102 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
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1 <tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy0">
0
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2 <description>to aligned read SAM/BAM records</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 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @PREPARE_REF@
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9 lofreq alnqual -b ${alnqual_choice.extended_baq} ${alnqual_choice.alnquals_to_use} $recompute_all '$reads' '$reference_fasta_fn' > '$output'
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10 ]]></command>
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11 <inputs>
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12 <param type="data" name="reads" format="bam" label="Reads" />
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13 <expand macro="reference_interface" />
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14 <expand macro="handle_alnqual" mode="Add" />
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15 <param argument="-r" name="recompute_all" type="boolean" truevalue="-r" falsevalue=""
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16 label="Overwrite exisitng values with newly computed ones" />
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="bam" label="${tool.name} to ${on_string}" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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24 <param name="ref_selector" value="history" />
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25 <param name="ref" ftype="fasta" value="pBR322.fa" />
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26 <output name="output" file="alnqual-out1.bam" />
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27 </test>
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28 <test>
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29 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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30 <param name="ref_selector" value="history" />
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31 <param name="ref" ftype="fasta" value="pBR322.fa" />
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32 <conditional name="alnqual_choice">
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33 <param name="alnquals_to_use" value="-B" />
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34 </conditional>
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35 <output name="output" file="alnqual-out2.bam" />
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36 </test>
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37 <test>
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38 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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39 <param name="ref_selector" value="history" />
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40 <param name="ref" ftype="fasta" value="pBR322.fa" />
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41 <conditional name="alnqual_choice">
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42 <param name="alnquals_to_use" value="-A" />
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43 </conditional>
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44 <output name="output" file="alnqual-out3.bam" />
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45 </test>
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46 <test>
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47 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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48 <param name="ref_selector" value="history" />
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49 <param name="ref" ftype="fasta" value="pBR322.fa" />
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50 <conditional name="alnqual_choice">
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51 <param name="extended_baq" value="false" />
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52 </conditional>
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53 <output name="output" file="alnqual-out4.bam" />
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54 </test>
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55 <test>
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56 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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57 <param name="ref_selector" value="history" />
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58 <param name="ref" ftype="fasta" value="pBR322.fa" />
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59 <param name="recompute" value="true" />
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60 <output name="output" file="alnqual-out5.bam" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to
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65 aligned read records
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66
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67 .. class:: infomark
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68
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69 **What it does**
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70
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71 This tool can compute base- and/or indel-alignment quality scores for aligned
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72 reads in SAM/BAM format and store these scores under the custom tags ``lb``
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73 (for the base alignment qualities, ``ai`` (insertion alignment qualities) and
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74 ``ad`` (deletion alignment qualities), which it will add to its output BAM.
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75
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76 These tags and their scores can be reused by LoFreq call, which can
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77 incorporate them into its model for variant quality calculation.
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78
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79 .. class:: warning
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80
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81 **Do not realign** your reads after adding alignment qualities to them since
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82 the scores would not be updated in the process!
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83
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84 Notes:
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85
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86 - While LoFreq call can optionally calculate the exact same scores on the fly
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87 if needed, having the scores added to the aligned read records is going to
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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88 save computation time with repeated variant calling from the same input data.
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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89
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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90 - The base alignment quality scores have the same meaning as in samtools, but
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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91 are expressed as absolute scores, not as base quality offsets like with the
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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92 `BQ` tag generated by samtools.
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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93
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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94 - `ai` and `ad` tags, if requested, will only be added to reads containing
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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95 insertions/deletions.
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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96 ]]></help>
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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97 <expand macro="citations" />
606542a18f82 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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98 </tool>