Mercurial > repos > galaxyp > dbbuilder

annotate dbbuilder.xml @ 6:3425a176dff2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"
author galaxyp
date Sun, 13 Sep 2020 08:33:43 +0000
parents cc23650fc85e
children 8e263cd38da1
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3425a176dff2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.1">
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2 <description></description>
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3 <requirements>
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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 </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. -->
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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)
0
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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"
3
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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'
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25 #set $type = "direct"
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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)
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28 #if str($source.annotation).endswith('.tar.gz'):
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29 #set $type = "tgz"
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30 #elif str($source.annotation).endswith('.zip'):
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31 #set $type = "zip"
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32 #end if
0
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33 #elif $source.from == "url"
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34 #set $url = $source.url
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35 #set $type = $source.archive_type
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36 #end if
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37 #if $type =="direct"
3
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38 wget -nv '$url' -O '${output_database}' --no-check-certificate
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39 #elif $type =="zip"
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40 wget -nv '$url' -O tmp.zip --no-check-certificate && zcat -c tmp.zip > '${output_database}'
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41 #elif $type =="gzip"
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42 wget -nv '$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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43 #elif $type =="bzip2"
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44 wget -nv '$url' -O tmp.bz2 --no-check-certificate && bzcat tmp.bz2 > '${output_database}'
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45 #elif $type =="tgz"
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46 wget -nv '$url' -O tmp.tar.gz && tar zxfO tmp.tar.gz > '${output_database}'
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47 #elif $type =="tbz"
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48 wget -nv '$url' -O tmp.tar.bz && tar jxfO tmp.tar.bz > '${output_database}'
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49 #end if
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50 ]]>
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51 </command>
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52 <inputs>
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53 <conditional name="source">
3
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54 <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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55 <option value="uniprot">UniProtKB</option>
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56 <option value="cRAP">cRAP (contaminants)</option>
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57 <option value="HMP">Human Microbiome Project body sites</option>
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58 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
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59 <option value="url">Custom URL</option>
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60 </param>
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61 <when value="uniprot">
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62 <param name="taxon" type="select" format="text" help="select species for protein database">
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63 <label>Taxonomy</label>
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64 <options from_file="uniprot_taxons.loc">
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65 <column name="name" index="0" />
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66 <column name="value" index="1" />
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67 </options>
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68 </param>
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69 <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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70 <option value="+">UniProtKB</option>
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71 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
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72 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
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73 <sanitizer>
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74 <valid>
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75 <add value="%"/>
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76 </valid>
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77 </sanitizer>
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78 </param>
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79 <param name="set" type="select" label="Proteome Set">
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80 <option value="+">Any</option>
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81 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
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82 <option value="+keyword%3a181">Complete Proteome Set</option>
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83 <sanitizer>
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84 <valid>
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85 <add value="%"/>
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86 </valid>
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87 </sanitizer>
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88 </param>
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89 <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" />
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90 </when>
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91 <when value="cRAP" />
3
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92 <when value="HMP">
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93 <param name="site" type="select" label="Proteome for body site">
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94 <option value="Airways">HMP airways</option>
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95 <option value="Blood">HMP Blood</option>
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96 <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
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97 <option value="Oral">HMP Oral</option>
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98 <option value="Skin">HMP Skin</option>
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99 <option value="Urogenital_tract">HMP urogenital Tract</option>
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100 </param>
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101 </when>
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102 <when value="HOMD">
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103 <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
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104 <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
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105 <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>
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106 </param>
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107 </when>
0
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108 <when value="url">
3
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109 <param name="url" value="" type="text" label="URL (http, ftp) of Fasta sequences">
0
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110 <sanitizer>
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111 <valid>
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112 <add value="%"/>
4
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113 <add value="~"/>
0
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114 </valid>
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115 </sanitizer>
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116 </param>
3
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117 <param name="archive_type" type="select" label="Fasta source compression type">
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118 <option value="direct" selected="true">fasta file (uncompressed)</option>
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119 <option value="gzip">fasta.gz (gzip compressed)</option>
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120 <option value="bzip2">fasta.bz2 (bzip2 compressed)</option>
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121 <option value="zip">fasta.zip or fasta.Z (Zip compressed)</option>
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122 <option value="tgz">fasta.tgz or fasta.tar.gz (tar archive gzip compressed)</option>
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123 <option value="tbz">fasta.tbz or fasta.tar.bz (tar archive bzip2 compressed)</option>
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124 </param>
0
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125 </when>
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126 </conditional>
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127 </inputs>
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128 <outputs>
3
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129 <data format="fasta" name="output_database" label="Protein Database ${source.from}" />
0
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130 </outputs>
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131 <tests>
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132 <test>
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133 <param name="from" value="cRAP" />
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134 <output name="output_database">
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135 <assert_contents>
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136 <has_text text="KKA1_ECOLX" />
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137 </assert_contents>
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138 </output>
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139 </test>
5
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140 <test>
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141 <param name="from" value="url" />
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142 <param name="url" value="https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" />
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143 <param name="archive_type" value="direct" />
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144 <output name="output_database">
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145 <assert_contents>
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146 <has_text text="KKA1_ECOLX" />
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147 </assert_contents>
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148 </output>
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149 </test>
0
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150 </tests>
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151 <help>
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152 <![CDATA[
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153 **Output**
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154
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155 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.
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156
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157 **External Links**
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158
3
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159 - Galaxy-P_101_ shows usage Protein Database Downloader tool in the creation of a workflow
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160 - UniProtKB_ provides additional information about the UniProt Knowledgebase
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161
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162
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163 .. _Galaxy-P_101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
0
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164 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb
3
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165
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166
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167 **Additional Protein Fasta URLs**
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168
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169 *HUMAN GUT METAPROTEOME:*
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170
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171 * 61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz
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174 *MOUSE GUT MICROBIOTA:*
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175
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176 * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP
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178
0
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179 ]]>
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180 </help>
3
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181 <citations>
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182 <citation type="doi">10.1093/nar/gkw1099</citation>
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183 <citation type="doi">10.1093/nar/gkv1195 </citation>
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184 <citation type="doi">10.1093/database/baq013</citation>
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185 <citation type="doi">10.1038/nature11209</citation>
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186 <citation type="doi">10.1038/nature11234</citation>
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187 </citations>
0
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188 </tool>
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189