Mercurial > repos > jjohnson > mzsqlite_psm_align

annotate mzsqlite_psm_align.xml @ 4:a96b2754171c draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 35eb22a121f8bc6378610bfc85e899171cc6441c-dirty
author jjohnson
date Tue, 10 Apr 2018 10:55:22 -0400
parents ce4174c80be5
children af5f22779a8e
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1 <tool id="mzsqlite_psm_align" name="MzSQLite ProBED ProBAM" version="0.1.0">
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2 <description>from mz.sqlite aand genomic mapping</description>
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3 <requirements>
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4 <requirement type="package">biopython</requirement>
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5 <requirement type="package">twobitreader</requirement>
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6 <requirement type="package">pysam</requirement>
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7 <requirement type="package">gffutils</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python '$__tool_directory__/mzsqlite_psm_align.py'
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11 #if $ref.ref_source == 'cached':
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12 --twobit='$ref.ref_loc.fields.path'
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13 #elif $ref.ref_source == 'history':
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14 --twobit='$ref.ref_file'
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15 #end if
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16 #if $gffutilsdb:
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17 --gffutils_file '$gffutilsdb'
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18 #end if
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19 #if $readlignments:
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20 --reads_bam '$readlignments'
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21 #end if
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22 #if 'probed' in str($output_formats).split(','):
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23 --probed '$probed'
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24 #end if
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25 #if 'prosam' in str($output_formats).split(','):
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26 --prosam '$prosam'
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27 #end if
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28 #if 'probam' in str($output_formats).split(','):
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29 --probam '$probam'
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30 #end if
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31 #if $genomicref:
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32 --genomeReference $genomicref
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33 #else
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34 --genomeReference $genomicdb.metadata.dbkey
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35 #end if
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36 '$mzsqlitedb' '$genomicdb'
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37 ]]></command>
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38 <inputs>
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39 <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite databse"/>
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40 <param name="genomicdb" type="data" format="sqlite" label="genomic mapping sqlite databse"/>
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41 <conditional name="ref">
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42 <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
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43 <option value="cached">Locally cached twobit</option>
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44 <option value="history">History dataset twobit</option>
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45 </param>
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46 <when value="cached">
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47 <param name="ref_loc" type="select" label="Select reference 2bit file">
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48 <options from_data_table="twobit" />
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
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53 </when>
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54 </conditional>
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55 <param name="gffutilsdb" type="data" format="sqlite" label="gffutils sqlite database" optional="true"/>
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56 <param name="readlignments" type="data" format="bam" label="read alignments bam" optional="true"/>
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57 <param name="genomicref" type="text" value="" label="Genome Reference name" optional="true"/>
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58 <param name="output_formats" type="select" display="checkboxes" label="outputs" multiple="true">
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59 <option value="probam">pro.bam</option>
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60 <option value="prosam">pro.sam</option>
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61 <option value="probed">pro.bed</option>
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62 </param>
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63 </inputs>
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64 <outputs>
4
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65 <data name="prosam" format="sam">
0
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66 <filter>'prosam' in output_formats</filter>
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67 </data>
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68 <data name="probam" format="pro.bam">
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69 <filter>'probam' in output_formats</filter>
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70 </data>
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71 <data name="probed" format="pro.bed">
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72 <filter>'probed' in output_formats</filter>
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73 </data>
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74 </outputs>
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75 <help><![CDATA[
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76
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77 Generates proBAM or proBED feature alignment files for peptides identified from a mass spectrometry protein search analysis.
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78
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79 The tool mz_to_sqlite generates the a SQLite database for a mzIdentML file,
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80 along with the fasta search database and the spectrum files used in the search.
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81
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82 The genomic mapping sqlite database has this schema:
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83
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84 CREATE TABLE feature_cds_map ( /* One row for each exon in the search protein */
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85 name TEXT, /* Accession name of search protein in mzIdentML */
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86 chrom TEXT, /* Reference genome chromosome for this exon */
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87 start INTEGER, /* genomic start of the exon (zero-based like BED) */
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88 end INTEGER, /* genomic end of the exon (non-incluse like BED) */
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89 strand TEXT, /* genomic strand: '+' or '-' */
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90 cds_start INTEGER, /* The CDS coding start for this exon (zero-based) */
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91 cds_end INTEGER /* The CDS coding start end this exon (non-inclusive) */
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92 );
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93
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94 Example:
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95 sqlite> select * from feature_cds_map WHERE name like 'ENSMUSP00000000001%';
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96 ENSMUSP00000000001 chr3 108145887 108146005 - 0 118
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97 ENSMUSP00000000001 chr3 108123794 108123837 - 118 161
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98 ENSMUSP00000000001 chr3 108123541 108123683 - 161 303
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99 ENSMUSP00000000001 chr3 108118300 108118458 - 303 461
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100 ENSMUSP00000000001 chr3 108115762 108115891 - 461 590
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101 ENSMUSP00000000001 chr3 108112472 108112602 - 590 720
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102 ENSMUSP00000000001 chr3 108111934 108112088 - 720 874
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103 ENSMUSP00000000001 chr3 108109421 108109612 - 874 1065
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104
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105 This schema can describe structural variants as well as canonical transcripts.
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106
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107 ]]></help>
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108 </tool>