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annotate dbbuilder.xml @ 8:3f6354b7eb94 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
author galaxyp
date Tue, 27 Sep 2022 13:21:28 +0000
parents 8e263cd38da1
children 0f641df3f28a
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3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.3">
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2 <description></description>
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3 <requirements>
6
3425a176dff2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"
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4 <requirement type="package" version="1.20.1">wget</requirement>
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5 <requirement type="package" version="3.8">python</requirement>
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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6 <requirement type="package" version="2.20.1">requests</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error downloading database." />
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10 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
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11 </stdio>
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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12 <!-- TODO: escape quotes. -->
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13 <!-- Add NCBI and maxquant contaminants. -->
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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14 <!-- http://maxquant.org/contaminants.zip -->
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15 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
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16 <command>
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17 <![CDATA[
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18 #if $source.from == "uniprot"
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19 #if $source.set:
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20 #set $modified_set = '&' + str($source.set)
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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21 #else
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22 #set $modified_set = ''
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23 #end if
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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24 #if $source.taxon_id
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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25 #set $taxon_id = $source.taxon_id
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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26 #else
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27 #set $taxon_id = $source.taxon
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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28 #end if
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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29 #set $url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=taxonomy_id:"' + str($taxon_id) + '"' + str($modified_set) + str($source.reviewed) + str($source.include_isoform)
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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30 #set $type = "uniprotkb_stream"
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31 #elif $source.from == "cRAP"
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32 ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
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33 #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta"
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34 #set $type = "direct"
3
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35 #elif $source.from == "HMP"
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36 #set $url = 'http://downloads.hmpdacc.org/data/reference_genomes/body_sites/' + str($source.site) + '.pep.fsa'
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37 #set $type = "direct"
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38 #elif $source.from == "HOMD"
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39 #set $url = 'ftp://ftp.homd.org/human_oral_microbial_genomic_sequences/current/' + str($source.annotation)
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40 #if str($source.annotation).endswith('.tar.gz'):
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41 #set $type = "tgz"
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42 #elif str($source.annotation).endswith('.zip'):
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43 #set $type = "zip"
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44 #end if
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45 #elif $source.from == "url"
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46 #set $url = $source.url
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47 #set $type = $source.archive_type
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48 #end if
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49 #if $type =="uniprotkb_stream"
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50 python '$__tool_directory__/uniprotkb.py' --url '$url' -o 'tmp.gz' && gzip -dc 'tmp.gz' > '${output_database}'
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51 #elif $type =="direct"
3
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52 wget -nv '$url' -O '${output_database}' --no-check-certificate
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53 #elif $type =="zip"
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54 wget -nv '$url' -O tmp.zip --no-check-certificate && zcat -c tmp.zip > '${output_database}'
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55 #elif $type =="gzip"
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56 wget -nv '$url' -O tmp.gz --no-check-certificate && (if `command -v gzcat > /dev/null`; then gzcat tmp.gz; else zcat tmp.gz ; fi) > '${output_database}'
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57 #elif $type =="bzip2"
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58 wget -nv '$url' -O tmp.bz2 --no-check-certificate && bzcat tmp.bz2 > '${output_database}'
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59 #elif $type =="tgz"
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60 wget -nv '$url' -O tmp.tar.gz && tar zxfO tmp.tar.gz > '${output_database}'
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61 #elif $type =="tbz"
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62 wget -nv '$url' -O tmp.tar.bz && tar jxfO tmp.tar.bz > '${output_database}'
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63 #end if
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64 ]]>
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65 </command>
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66 <inputs>
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67 <conditional name="source">
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68 <param name="from" type="select" label="Download from"
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69 help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a cross species collection of functional protein databases">
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70 <option value="uniprot">UniProtKB</option>
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71 <option value="cRAP">cRAP (contaminants)</option>
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72 <option value="HMP">Human Microbiome Project body sites</option>
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73 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
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74 <option value="url">Custom URL</option>
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75 </param>
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76 <when value="uniprot">
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77 <param name="taxon" type="select" format="text" help="select species for protein database">
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78 <label>Taxonomy</label>
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79 <options from_file="uniprot_taxons.loc">
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80 <column name="name" index="0" />
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81 <column name="value" index="1" />
8
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82 <filter type="add_value" name="Escherichia coli (strain K12)" value="83333" />
0
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83 </options>
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84 </param>
8
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85 <param name="taxon_id" type="integer" value="" min="1" optional="true" help="Specify a NCBI taxon id to override species selection"/>
0
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86 <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy">
8
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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87 <option value="">UniProtKB</option>
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
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88 <option value="+reviewed%3Atrue">UniProtKB/Swiss-Prot (reviewed only)</option>
3f6354b7eb94 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
galaxyp
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89 <option value="+reviewed%3Afalse">UniProtKB/TrEMBL (unreviewed only)</option>
0
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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90 <sanitizer>
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91 <valid>
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
galaxyp
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92 <add value="%"/>
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93 </valid>
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94 </sanitizer>
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95 </param>
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96 <param name="set" type="select" label="Proteome Set">
8
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97 <option value="">Any</option>
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98 <option value="keyword%3aKW-1185" selected="true">Reference Proteome Set</option>
0
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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99 <sanitizer>
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100 <valid>
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101 <add value="%"/>
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102 </valid>
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103 </sanitizer>
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104 </param>
8
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105 <param name="include_isoform" type="boolean" truevalue="&amp;includeIsoform=true" falsevalue=""
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106 label="Include isoform data" help="several different forms of a given protein are incorporated into database" />
0
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107 </when>
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108 <when value="cRAP" />
3
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109 <when value="HMP">
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110 <param name="site" type="select" label="Proteome for body site">
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111 <option value="Airways">HMP airways</option>
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112 <option value="Blood">HMP Blood</option>
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113 <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
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114 <option value="Oral">HMP Oral</option>
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115 <option value="Skin">HMP Skin</option>
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116 <option value="Urogenital_tract">HMP urogenital Tract</option>
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117 </param>
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118 </when>
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119 <when value="HOMD">
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120 <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
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121 <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
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galaxyp
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122 <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>
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123 </param>
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124 </when>
0
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125 <when value="url">
3
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126 <param name="url" value="" type="text" label="URL (http, ftp) of Fasta sequences">
0
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127 <sanitizer>
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128 <valid>
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129 <add value="%"/>
4
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130 <add value="~"/>
0
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131 </valid>
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132 </sanitizer>
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133 </param>
3
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134 <param name="archive_type" type="select" label="Fasta source compression type">
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135 <option value="direct" selected="true">fasta file (uncompressed)</option>
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136 <option value="gzip">fasta.gz (gzip compressed)</option>
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137 <option value="bzip2">fasta.bz2 (bzip2 compressed)</option>
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138 <option value="zip">fasta.zip or fasta.Z (Zip compressed)</option>
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139 <option value="tgz">fasta.tgz or fasta.tar.gz (tar archive gzip compressed)</option>
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140 <option value="tbz">fasta.tbz or fasta.tar.bz (tar archive bzip2 compressed)</option>
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141 </param>
0
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142 </when>
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143 </conditional>
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144 </inputs>
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145 <outputs>
3
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146 <data format="fasta" name="output_database" label="Protein Database ${source.from}" />
0
ab1148688233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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147 </outputs>
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148 <tests>
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149 <test>
8
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150 <conditional name="source">
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151 <param name="from" value="cRAP" />
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152 </conditional>
0
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153 <output name="output_database">
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154 <assert_contents>
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155 <has_text text="KKA1_ECOLX" />
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156 </assert_contents>
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157 </output>
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158 </test>
5
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159 <test>
8
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160 <conditional name="source">
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161 <param name="from" value="uniprot" />
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162 <param name="taxon" value="83333"/>
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163 <param name="taxon_id" value="2697049"/>
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164 </conditional>
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165 <output name="output_database">
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166 <assert_contents>
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167 <has_text text="SPIKE_SARS2" />
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168 </assert_contents>
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169 </output>
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170 </test>
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171 <test>
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172 <conditional name="source">
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173 <param name="from" value="uniprot" />
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174 <param name="taxon_id" value="2697049"/>
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175 <param name="reviewed" value="+reviewed%3Atrue"/>
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176 <param name="set" value=""/>
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177 </conditional>
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178 <output name="output_database">
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179 <assert_contents>
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180 <has_text text=">sp|P0DTC1|R1A_SARS2" />
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181 <not_has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" />
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182 </assert_contents>
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183 </output>
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184 </test>
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185 <test>
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186 <conditional name="source">
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187 <param name="from" value="uniprot" />
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188 <param name="taxon_id" value="2697049"/>
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189 <param name="reviewed" value="+reviewed%3Afalse"/>
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190 <param name="set" value=""/>
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191 </conditional>
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192 <output name="output_database">
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193 <assert_contents>
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194 <has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" />
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195 <not_has_text text=">sp|P0DTC1|R1A_SARS2" />
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196 </assert_contents>
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197 </output>
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198 </test>
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199
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200 <test>
5
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201 <param name="from" value="url" />
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202 <param name="url" value="https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" />
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203 <param name="archive_type" value="direct" />
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204 <output name="output_database">
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205 <assert_contents>
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206 <has_text text="KKA1_ECOLX" />
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207 </assert_contents>
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208 </output>
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209 </test>
0
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210 </tests>
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211 <help>
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212 <![CDATA[
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213 **Output**
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214
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215 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.
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216
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217 **External Links**
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218
3
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219 - Galaxy-P_101_ shows usage Protein Database Downloader tool in the creation of a workflow
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220 - UniProtKB_ provides additional information about the UniProt Knowledgebase
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221
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222
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223 .. _Galaxy-P_101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
0
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224 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb
3
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225
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226
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227 **Additional Protein Fasta URLs**
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228
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229 *HUMAN GUT METAPROTEOME:*
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230
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231 * 61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz
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232
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233
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234 *MOUSE GUT MICROBIOTA:*
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235
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236 * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP
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237
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238
0
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239 ]]>
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240 </help>
3
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241 <citations>
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242 <citation type="doi">10.1093/nar/gkw1099</citation>
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243 <citation type="doi">10.1093/nar/gkv1195 </citation>
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244 <citation type="doi">10.1093/database/baq013</citation>
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245 <citation type="doi">10.1038/nature11209</citation>
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246 <citation type="doi">10.1038/nature11234</citation>
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247 </citations>
0
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248 </tool>
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249