Mercurial > repos > galaxyp > mzsqlite_psm_align

annotate mzsqlite_psm_align.xml @ 0:f2dc9805107a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
author galaxyp
date Mon, 16 Apr 2018 18:00:53 -0400
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children 4f8cf8fbef57
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f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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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 #if $readlignments:
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11 ln -s -f '${$readlignments}' 'input.bam' &&
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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12 ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' &&
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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13 #end if
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14 python '$__tool_directory__/mzsqlite_psm_align.py'
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15 #if $ref.ref_source == 'cached':
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16 --twobit='$ref.ref_loc.fields.path'
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17 #elif $ref.ref_source == 'history':
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18 --twobit='$ref.ref_file'
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19 #end if
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20 #if $gffutilsdb:
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21 --gffutils_sqlite '$gffutilsdb'
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22 #end if
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23 #if $readlignments:
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24 --reads_bam 'input.bam'
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25 #end if
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26 #if 'probed' in str($output_formats).split(','):
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27 --probed '$probed'
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28 #end if
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29 #if 'prosam' in str($output_formats).split(','):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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30 --prosam '$prosam'
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31 #end if
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32 #if 'probam' in str($output_formats).split(','):
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33 --probam '$probam'
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34 #end if
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35 #if $genomicref:
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36 --genomeReference $genomicref
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37 #else
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38 --genomeReference $genomicdb.metadata.dbkey
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39 #end if
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40 -v
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41 '$mzsqlitedb' '$genomicdb'
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42 ]]></command>
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43 <inputs>
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44 <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite databse"/>
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45 <param name="genomicdb" type="data" format="sqlite" label="genomic mapping sqlite databse"/>
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46 <conditional name="ref">
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47 <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
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48 <option value="cached">Locally cached twobit</option>
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49 <option value="history">History dataset twobit</option>
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50 </param>
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51 <when value="cached">
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52 <param name="ref_loc" type="select" label="Select reference 2bit file">
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53 <options from_data_table="twobit" />
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54 </param>
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55 </when>
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56 <when value="history">
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57 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
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58 </when>
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59 </conditional>
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60 <param name="gffutilsdb" type="data" format="sqlite" label="gffutils sqlite database" optional="true"/>
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61 <param name="readlignments" type="data" format="bam" label="read alignments bam" optional="true"/>
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62 <param name="genomicref" type="text" value="" label="Genome Reference name" optional="true"/>
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63 <param name="output_formats" type="select" display="checkboxes" label="outputs" multiple="true">
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64 <option value="probam">pro.bam</option>
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65 <option value="prosam">pro.sam</option>
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66 <option value="probed">pro.bed</option>
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
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71 <filter>'prosam' in output_formats</filter>
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72 </data>
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73 <data name="probam" format="bam" label="pro.Bam on ${on_string}">
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74 <filter>'probam' in output_formats</filter>
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75 </data>
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76 <data name="probed" format="bed" label="pro.Bed on ${on_string}">
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77 <filter>'probed' in output_formats</filter>
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78 </data>
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79 </outputs>
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80 <help><![CDATA[
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81
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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82 Generates proBAM or proBED feature alignment files for peptides identified from a mass spectrometry protein search analysis.
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83
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84 The tool mz_to_sqlite generates the a SQLite database for a mzIdentML file,
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85 along with the fasta search database and the spectrum files used in the search.
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86
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87 The genomic mapping sqlite database has this schema:
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88
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89 CREATE TABLE feature_cds_map ( /* One row for each exon in the search protein */
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90 name TEXT, /* Accession name of search protein in mzIdentML */
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91 chrom TEXT, /* Reference genome chromosome for this exon */
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92 start INTEGER, /* genomic start of the exon (zero-based like BED) */
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93 end INTEGER, /* genomic end of the exon (non-incluse like BED) */
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94 strand TEXT, /* genomic strand: '+' or '-' */
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95 cds_start INTEGER, /* The CDS coding start for this exon (zero-based) */
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96 cds_end INTEGER /* The CDS coding start end this exon (non-inclusive) */
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97 );
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98
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99 Example:
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100 sqlite> select * from feature_cds_map WHERE name like 'ENSMUSP00000000001%';
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101 ENSMUSP00000000001 chr3 108145887 108146005 - 0 118
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102 ENSMUSP00000000001 chr3 108123794 108123837 - 118 161
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103 ENSMUSP00000000001 chr3 108123541 108123683 - 161 303
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104 ENSMUSP00000000001 chr3 108118300 108118458 - 303 461
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105 ENSMUSP00000000001 chr3 108115762 108115891 - 461 590
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106 ENSMUSP00000000001 chr3 108112472 108112602 - 590 720
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107 ENSMUSP00000000001 chr3 108111934 108112088 - 720 874
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108 ENSMUSP00000000001 chr3 108109421 108109612 - 874 1065
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109
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110 This schema can describe structural variants as well as canonical transcripts.
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111
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112 ]]></help>
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113 </tool>