Mercurial > repos > galaxyp > dbbuilder

annotate dbbuilder.xml @ 8:a85fbebe8b2f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
author galaxyp
date Wed, 03 May 2017 09:53:17 -0400
parents a94dc3d469cb
children c1b437242fee
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a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package">gnu-wget</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error downloading database." />
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8 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
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9 </stdio>
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10 <!-- TODO: escape quotes. -->
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11 <!-- Add NCBI and maxquant contaminants. -->
1d3557cec567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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12 <!-- http://maxquant.org/contaminants.zip -->
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13 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
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14 <command>
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15 <![CDATA[
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16 #if $source.from == "uniprot"
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17 #set $url = 'http://www.uniprot.org/uniprot/?query=taxonomy:"' + str($source.taxon) + '"' + str($source.set) + str($source.reviewed) + '&force=yes&format=fasta' + str($source.include_isoform)
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18 #set $type = "direct"
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19 #elif $source.from == "cRAP"
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20 ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
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21 #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta"
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22 #set $type = "direct"
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23 #elif $source.from == "HMP"
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24 #set $url = 'http://downloads.hmpdacc.org/data/reference_genomes/body_sites/' + str($source.site) + '.pep.fsa'
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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25 #set $type = "direct"
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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26 #elif $source.from == "HOMD"
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27 #set $url = 'ftp://ftp.homd.org/human_oral_microbial_genomic_sequences/current/' + str($source.annotation)
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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28 #if str($source.annotation).endswith('.tar.gz'):
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29 #set $type = "tgz"
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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30 #elif str($source.annotation).endswith('.zip'):
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31 #set $type = "zip"
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32 #end if
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33 #elif $source.from == 'EBI Metagenomics'
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34 #set $url = 'https://www.ebi.ac.uk/metagenomics/projects/' + str($source.ebi_project) + '/samples/' + str($source.ebi_sample) + '/runs/' + str($source.ebi_run) + '/results/versions/' + str($source.ebi_version) + '/sequences/' + str($source.ebi_annotation) + '/chunks/1'
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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35 #set $type = "gzip"
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36 #elif $source.from == "url"
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37 #set $url = $source.url
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38 #set $type = $source.archive_type
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39 #end if
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40 #if $type =="direct"
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41 wget -nv '$url' -O '${output_database}' --no-check-certificate
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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42 #elif $type =="zip"
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43 wget -nv '$url' -O tmp.zip --no-check-certificate && zcat -c tmp.zip > '${output_database}'
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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44 #elif $type =="gzip"
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45 wget -nv '$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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46 #elif $type =="bzip2"
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47 wget -nv '$url' -O tmp.bz2 --no-check-certificate && bzcat tmp.bz2 > '${output_database}'
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48 #elif $type =="tgz"
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49 wget -nv '$url' -O tmp.tar.gz && tar zxfO tmp.tar.gz > '${output_database}'
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50 #elif $type =="tbz"
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51 wget -nv '$url' -O tmp.tar.bz && tar jxfO tmp.tar.bz > '${output_database}'
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52 #end if
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53 ]]>
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54 </command>
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55 <inputs>
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56 <conditional name="source">
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57 <param name="from" type="select" label="Download from" 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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58 <option value="uniprot">UniProtKB</option>
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59 <option value="cRAP">cRAP (contaminants)</option>
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60 <option value="HMP">Human Microbiome Project body sites</option>
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61 <option value="EBI Metagenomics">EBI Metagenomics</option>
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62 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
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63 <option value="url">Custom URL</option>
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64 </param>
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65 <when value="uniprot">
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66 <param name="taxon" type="select" format="text" help="select species for protein database">
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67 <label>Taxonomy</label>
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68 <options from_file="uniprot_taxons.loc">
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69 <column name="name" index="0" />
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70 <column name="value" index="1" />
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71 </options>
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72 </param>
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73 <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">
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74 <option value="+">UniProtKB</option>
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75 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
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76 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
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77 <sanitizer>
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78 <valid>
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79 <add value="%"/>
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 <param name="set" type="select" label="Proteome Set">
1d3557cec567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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84 <option value="+">Any</option>
1d3557cec567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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85 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
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86 <option value="+keyword%3a181">Complete Proteome Set</option>
1d3557cec567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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87 <sanitizer>
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88 <valid>
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89 <add value="%"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" />
1d3557cec567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
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94 </when>
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95 <when value="cRAP" />
8
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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96 <when value="HMP">
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97 <param name="site" type="select" label="Proteome for body site">
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98 <option value="Airways">HMP airways</option>
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99 <option value="Blood">HMP Blood</option>
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100 <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
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101 <option value="Oral">HMP Oral</option>
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102 <option value="Skin">HMP Skin</option>
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103 <option value="Urogenital_tract">HMP urogenital Tract</option>
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104 </param>
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105 </when>
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106 <when value="EBI Metagenomics">
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107 <param name="ebi_project" value="" type="text" label="EBI Metagenomics Project (e.g. DRP003095)">
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108 <help><![CDATA[
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109 Look up EBI Metagenomics at https://www.ebi.ac.uk/metagenomics/search
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110 ]]></help>
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111 </param>
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112 <param name="ebi_sample" value="" type="text" label="EBI Metagenomics Sample (e.g. DRS029200)">
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113 </param>
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114 <param name="ebi_run" value="" type="text" label="EBI Metagenomics Run (e.g. DRR033743)">
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115 </param>
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116 <param name="ebi_version" value="" type="text" label="EBI Metagenomics Pipeline Version (e.g. 3.0)">
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117 </param>
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118 <param name="ebi_annotation" type="boolean" label="With Annotation" checked="true"
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119 truevalue="PredictedCDSWithAnnotation" falsevalue="PredictedCDSWithioutAnnotation"/>
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120
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121 </when>
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122 <when value="HOMD">
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123 <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
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124 <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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125 <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>
a85fbebe8b2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
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126 </param>
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127 </when>
5
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128 <when value="url">
8
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129 <param name="url" value="" type="text" label="URL (http, ftp) of Fasta sequences">
5
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130 <sanitizer>
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131 <valid>
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132 <add value="%"/>
8
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133 <add value="~"/>
5
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134 </valid>
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135 </sanitizer>
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136 </param>
8
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137 <param name="archive_type" type="select" label="Fasta source compression type">
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138 <option value="direct" selected="true">fasta file (uncompressed)</option>
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139 <option value="gzip">fasta.gz (gzip compressed)</option>
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140 <option value="bzip2">fasta.bz2 (bzip2 compressed)</option>
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141 <option value="zip">fasta.zip or fasta.Z (Zip compressed)</option>
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142 <option value="tgz">fasta.tgz or fasta.tar.gz (tar archive gzip compressed)</option>
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143 <option value="tbz">fasta.tbz or fasta.tar.bz (tar archive bzip2 compressed)</option>
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144 </param>
5
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145 </when>
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146 </conditional>
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147 </inputs>
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148 <outputs>
8
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149 <data format="fasta" name="output_database" label="Protein Database ${source.from}" />
5
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150 </outputs>
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151 <tests>
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152 <test>
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153 <param name="from" value="cRAP" />
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154 <output name="output_database">
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155 <assert_contents>
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156 <has_text text="KKA1_ECOLX" />
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157 </assert_contents>
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158 </output>
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159 </test>
8
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160 <test>
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161 <param name="from" value="url" />
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162 <param name="url" value="https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" />
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163 <param name="archive_type" value="direct" />
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164 <output name="output_database">
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165 <assert_contents>
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166 <has_text text="KKA1_ECOLX" />
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167 </assert_contents>
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168 </output>
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169 </test>
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170 <test>
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171 <param name="from" value="EBI Metagenomics" />
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172 <param name="ebi_project" value="DRP003095" />
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173 <param name="ebi_sample" value="DRS029200" />
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174 <param name="ebi_run" value="DRR033743" />
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175 <param name="ebi_version" value="3.0" />
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176 <output name="output_database">
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177 <assert_contents>
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178 <has_text text="DRR033743" />
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179 </assert_contents>
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180 </output>
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181 </test>
5
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182 </tests>
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183 <help>
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184 <![CDATA[
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185 **Output**
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186
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187 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.
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188
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189 **External Links**
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190
8
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191 - Galaxy-P_101_ shows usage Protein Database Downloader tool in the creation of a workflow
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192 - UniProtKB_ provides additional information about the UniProt Knowledgebase
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193
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194
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195 .. _Galaxy-P_101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
5
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196 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb
8
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197
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198
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199 **Additional Protein Fasta URLs**
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200
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201 *HUMAN GUT METAPROTEOME:*
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202
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203 * 512MB gzip ftp://public.genomics.org.cn/BGI/gutmeta/UniSet/UniGene.pep.gz
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204 * 61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz
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205
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206
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207 *MOUSE GUT MICROBIOTA:*
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208
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209 * 417MB gzip ftp://climb.genomics.cn/pub/10.5524/100001_101000/100114/Genecatalog/184sample_2.6M.GeneSet.pep.gz
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210 * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP
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211
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212
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213 ]]>
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214 </help>
8
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215 <citations>
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216 <citation type="doi">10.1093/nar/gkw1099</citation>
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217 <citation type="doi">10.1093/nar/gkv1195 </citation>
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218 <citation type="doi">10.1093/database/baq013</citation>
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219 <citation type="doi">10.1038/nature11209</citation>
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220 <citation type="doi">10.1038/nature11234</citation>
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221 </citations>
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222 </tool>
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223