Mercurial > repos > galaxyp > mzsqlite_psm_align

annotate mzsqlite_psm_align.xml @ 1:4f8cf8fbef57 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit b0c57cac4e558d974a16b14d4498cf8d4ba9e0c7
author galaxyp
date Thu, 19 Apr 2018 14:30:28 -0400
parents f2dc9805107a
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1 <tool id="mzsqlite_psm_align" name="MzSQLite ProBAM ProBED" version="0.1.0">
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2 <description>from mz.sqlite and genomic mapping</description>
0
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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>
1
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44 <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite database"
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45 help="generated from mzIndentML by mz_to_sqlite"/>
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46 <param name="genomicdb" type="data" format="sqlite" label="genomic mapping sqlite database"
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47 help="Genomic mapping for the Search proteins in the mzIdentML"/>
0
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48 <conditional name="ref">
1
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49 <param name="ref_source" type="select" label="Source for Genomic Sequence Data"
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50 help="Used to generate the genomic reference sequence for idenfied peptides">
0
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51 <option value="cached">Locally cached twobit</option>
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52 <option value="history">History dataset twobit</option>
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53 </param>
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54 <when value="cached">
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55 <param name="ref_loc" type="select" label="Select reference 2bit file">
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56 <options from_data_table="twobit" />
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57 </param>
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58 </when>
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59 <when value="history">
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60 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
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61 </when>
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62 </conditional>
1
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63 <param name="gffutilsdb" type="data" format="sqlite" label="gffutils sqlite database" optional="true"
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64 help="Categorizes the peptide by GTF feature for the proBAM XG tag" />
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65 <param name="readlignments" type="data" format="bam" label="read alignments bam" optional="true"
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66 help="Allows proBAM SEQ field to be modified with observed variants"/>
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67 <param name="genomicref" type="text" value="" label="Genome Reference name" optional="true"
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68 help="The genome reference name to use in the proBED genomeReferenceVersion column"/>
0
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69 <param name="output_formats" type="select" display="checkboxes" label="outputs" multiple="true">
1
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70 <option value="probam" selected="true">pro.bam</option>
0
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71 <option value="prosam">pro.sam</option>
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72 <option value="probed">pro.bed</option>
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73 </param>
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74 </inputs>
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75 <outputs>
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76 <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
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77 <filter>'prosam' in output_formats</filter>
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78 </data>
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79 <data name="probam" format="bam" label="pro.Bam on ${on_string}">
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80 <filter>'probam' in output_formats</filter>
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81 </data>
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82 <data name="probed" format="bed" label="pro.Bed on ${on_string}">
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83 <filter>'probed' in output_formats</filter>
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84 </data>
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85 </outputs>
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86 <help><![CDATA[
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87
1
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88 Generates proBAM_ or proBED_ feature alignment files for peptides identified from a mass spectrometry protein search analysis.
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89
0
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90
1
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91 The tool mz_to_sqlite_ generates the a SQLite database for a mzIdentML file,
0
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92 along with the fasta search database and the spectrum files used in the search.
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93 This mz.sqlite database is used in conjuction with a genomic mapping sqlite database
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94 to generate the proBAM_ or proBED_ feature alignment files.
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95
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96 The genomic mapping sqlite database has this schema:
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97
1
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98 ::
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99
0
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100 CREATE TABLE feature_cds_map ( /* One row for each exon in the search protein */
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101 name TEXT, /* Accession name of search protein in mzIdentML */
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102 chrom TEXT, /* Reference genome chromosome for this exon */
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103 start INTEGER, /* genomic start of the exon (zero-based like BED) */
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104 end INTEGER, /* genomic end of the exon (non-incluse like BED) */
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105 strand TEXT, /* genomic strand: '+' or '-' */
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106 cds_start INTEGER, /* The CDS coding start for this exon (zero-based) */
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107 cds_end INTEGER /* The CDS coding start end this exon (non-inclusive) */
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108 );
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109
1
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110
0
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111 Example:
1
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112
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113 ::
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114
0
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115 sqlite> select * from feature_cds_map WHERE name like 'ENSMUSP00000000001%';
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116 name chrom start end strand cds_start cds_end
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117 ENSMUSP00000000001 chr3 108145887 108146005 - 0 118
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118 ENSMUSP00000000001 chr3 108123794 108123837 - 118 161
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119 ENSMUSP00000000001 chr3 108123541 108123683 - 161 303
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120 ENSMUSP00000000001 chr3 108118300 108118458 - 303 461
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121 ENSMUSP00000000001 chr3 108115762 108115891 - 461 590
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122 ENSMUSP00000000001 chr3 108112472 108112602 - 590 720
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123 ENSMUSP00000000001 chr3 108111934 108112088 - 720 874
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124 ENSMUSP00000000001 chr3 108109421 108109612 - 874 1065
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125
1
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126 Each row represents an exon in the search protein.
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127 The locations: start,end, cds_start, and cds_end are **zero-based** like BED format.
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128
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129 The **name** field must match the **accession** name used in the mz.sqlite database
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130 and thus the mzIdentML search results file.
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131
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132 The protein positions are described in CDS base offsets rather than Animo Acids offsets
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133 to allow for codons being split across exons.
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134
0
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135 This schema can describe structural variants as well as canonical transcripts.
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136
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137 .. _proBAM: http://www.psidev.info/probam
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138 .. _proBED: http://www.psidev.info/probed
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139 .. _mz_to_sqlite: https://toolshed.g2.bx.psu.edu/view/galaxyp/mz_to_sqlite/e34bdac5b157
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140
0
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141 ]]></help>
1
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142 <citations>
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143 <citation type="doi">10.1186/s13059-017-1377-x</citation>
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144 </citations>
0
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145 </tool>