Mercurial > repos > proteore > proteore_data_manager

annotate data_manager/resource_building.xml @ 48:09d9fd9b2d8c draft

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"planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty"
author proteore
date Fri, 31 Jan 2020 15:51:40 +0000
parents f89ddc972ad4
children 1c40456be1db
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48
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1 <tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.31" tool_type="manage_data">
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2 <description>
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3 to create or update reference files for proteore tools
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4 </description>
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5 <requirements>
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6 <!--requirement type="package" version="1.8.2">sparqlwrapper</requirement-->
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command><![CDATA[
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12
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13 python $__tool_directory__/resource_building.py
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14 #if $database.database == "human_protein_atlas"
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15 --hpa "$database.tissues"
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16 #else if $database.database == "peptide_atlas"
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17 --peptideatlas="$database.tissues"
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18 --date="$database.date"
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19 #else if $database.database == "id_mapping"
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20 --id_mapping="$database.species"
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21 #else if $database.database == "PPI"
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22 --interactome="$database.base.interactome"
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23 #if $database.base.interactome == "biogrid"
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24 --species="$database.base.species"
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25 #end if
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26 #else if $database.database == "nextprot"
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27 --database=$database.database
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28 #end if
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29 --output "$output"
31
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30 --tool_data_path=$__tool_data_path__
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31
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32 ]]></command>
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33
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34 <inputs>
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35 <conditional name="database">
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36 <param name="database" type="select">
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37 <option value="human_protein_atlas">Human Protein Atlas</option>
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38 <option value="peptide_atlas">Peptide Atlas</option>
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39 <option value="id_mapping">ID mapping</option>
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40 <option value="PPI">Build protein interaction maps</option>
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41 <option value="nextprot">neXtProt</option>
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42 </param>
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43 <when value="human_protein_atlas">
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44 <param name="tissues" type="select" multiple="false" label="Please select tissue">
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45 <option value="HPA_normal_tissue">Normal tissue</option>
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46 <option value="HPA_pathology">Pathology</option>
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47 <option value="HPA_full_atlas">Full Atlas</option>
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48 <option value="HPA_RNA_tissue">RNA Tissue</option>
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49 </param>
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50 </when>
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51 <when value="peptide_atlas">
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52 <param name="tissues" type="select" multiple="false" label="Please select the tissue">
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53 <option value="432.Human_Adrenal_gland">Human Adrenal gland proteome</option>
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54 <option value="441.Human_Brain">Human Brain proteome</option>
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55 <option value="427.Human_Breast">Human Breast proteome</option>
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56 <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option>
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57 <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option>
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58 <option value="429.Human_Digestive_system">Human Digestive system proteome</option>
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59 <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome</option>
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60 <option value="418.Human_Heart">Human Heart proteome</option>
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61 <option value="424.Human_Kidney">Human Kidney proteome</option>
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62 <option value="425.Human_Liver">Human Liver proteome</option>
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63 <option value="419.Human_Lung">Human Lung proteome</option>
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64 <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option>
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65 <option value="420.Human_Pancreas">Human Pancreas proteome</option>
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66 <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option>
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67 <option value="421.Human_Spleen">Human Spleen proteome</option>
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68 <option value="463.Human_Testis">Human Testis proteome</option>
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69 <option value="422.Human_Urinary_bladder">Human Bladder proteome</option>
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70 <option value="423.Human_Urine">Human Urine proteome</option>
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71 </param>
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72 <param name="date" type="text" value="" label="enter the build date" help="for example: '2018-04'"/>
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73 </when>
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74 <when value="id_mapping">
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75 <param name="species" type="select" multiple="false" label="Please select the species">
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76 <option value="Human">Human (Homo sapiens)</option>
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77 <option value="Mouse">Mouse (Mus musculus)</option>
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78 <option value="Rat">Rat (Rattus norvegicus)</option>
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79 </param>
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80 </when>
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81 <when value="PPI">
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82 <conditional name="base">
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83 <param name="interactome" type="select" multiple="false" label="Please select interactome">
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84 <option value="biogrid">BioGRID</option>
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85 <option value="bioplex">Human Bioplex 2.0</option>
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86 <option value="humap">Human protein complex Map (Hu.map)</option>
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87 </param>
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88 <when value="biogrid">
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89 <param name="species" type="select" multiple="false" label="Please select the species">
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90 <option value="Human">Human (Homo sapiens)</option>
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91 <option value="Mouse">Mouse (Mus musculus)</option>
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92 <option value="Rat">Rat (Rattus norvegicus)</option>
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93 </param>
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94 </when>
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95 <when value="bioplex"/>
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96 <when value="humap"/>
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97 </conditional>
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98 </when>
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99 <when value="nextprot"/>
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100 </conditional>
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101 </inputs>
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102
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103 <outputs>
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104 <!--data format="tabular" name="output">
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105 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" ext="tabular" visible="true" assign_primary_output="true" />
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106 </data-->
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107 <data name="output" format="data_manager_json"/>
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108 </outputs>
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109
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110 <tests>
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111 </tests>
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112
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113 <help><![CDATA[
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114
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115 **Description**
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116
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117 This tool is a data manager designed to update resources files of ProteoRe tools. For now, only resources files for tools listed below are handled:
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118
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119 * "Get MS/MS observations in tissue/fluid [Peptide Atlas]"
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120 * "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]"
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121 * "ID converter"
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122
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123 -----
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124
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125 **Input**
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126
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127 There's no input needed, once you selected the tool and file you want to update, it will be generated automatically.
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128
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129 -----
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130
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131 **Parameters**
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132
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133 * database: the database to update (for now one per tool)
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134
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135 Once a database is selected, there's a second dropdown menu to select the specific file you want to update.
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136
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137 * for 'Human Protein Atlas': 'Normal tissue', 'Pathology' and 'Full Atlas'
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138
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139 * for 'Peptide Atlas': 'Human liver', 'Human brain', 'Human heart', 'Human kidney', 'Human blood plasma', 'Human urine' and 'Human cerebrospinal fluid'
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140
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141 * for 'ID mapping': 'Human (Homo sapiens)', 'Mouse (Mus musculus)' and 'Rat (Rattus norvegicus)'
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142
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143 * for 'Build protein interaction maps': "BioGRID", "Bioplex" and "Human (Homo sapiens)", "Mouse (Mus musculus)", "Rat (Rattus norvegicus)"
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144
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145 -----
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146
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147 **Output**
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148
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149 The output is the reference file selected for update in input.
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150
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151 For example, if you select database="Human Protein Atlas" and Please select tissue="Normal tissue":
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152
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153 the output is a new reference file for "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]"
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154 dated from the day and listed in the dropdown menu "Normal tissue HPA version".
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155
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156 .. class:: warningmark
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157
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158 A reference file created with this data manager will appears in the concerned ProteoRE tool. It can not be removed with the data manager.
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159
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160 -----
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161
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162 **Data sources**
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163
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164 For 'Human Protein Atlas':
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165
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166 * `Normal Tissue <https://www.proteinatlas.org/download/normal_tissue.tsv.zip>`_.
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167 * `Pathology <https://www.proteinatlas.org/download/pathology.tsv.zip>`_.
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168 * `Full Atlas <https://www.proteinatlas.org/download/proteinatlas.tsv.zip>`_.
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169
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170 For 'Peptide Atlas':
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171
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172
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173 * `Human Adrenal gland proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=432&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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174 * `Human Brain proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=441&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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175 * `Human Breast Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=427&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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176 * `Human CSF proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=434&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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177 * `Human Digestive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=429&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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178 * `Human female reproductive system proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=430&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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179 * `Human Heart proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=418&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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180 * `Human Kidney man Kidney Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=424&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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181 * `Human Liver proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=425&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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182 * `Human Lung proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=419&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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183 * `Human Male Reproductive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=431&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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184 * `Human Pancreas proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=420&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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185 * `Human Plasma Non-Glyco proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=465&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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186 * `Human Spleen proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=421&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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187 * `Human Testis proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=463&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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188 * `Human Urinary Bladder proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=422&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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189 * `Human Urine proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=423&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
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190
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191 For ID mapping:
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192
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193 * `HUMAN_9606_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz>`_.
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194 * `HUMAN_9606_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz>`_.
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195 * `nextprot_ac_list_all.txt <ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt>`_.
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196 * `MOUSE_10090_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping_selected.tab.gz>`_.
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197 * `MOUSE_10090_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz>`_.
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198 * `RAT_10116_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping_selected.tab.gz>`_.
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199 * `RAT_10116_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping.dat.gz>`_.
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200
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201 For Build protein interaction maps:
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202
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203 * `BIOGRID_oragism <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.167/BIOGRID-ORGANISM-3.5.167.tab2.zip>`_.
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204 * `NCBI2Reactome.txt <https://www.reactome.org/download/current/NCBI2Reactome.txt>`_.
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205 * `Bioplex_interactionList_v4a.tsv <http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv>`_.
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206 * `UniProt2Reactome.txt <https://reactome.org/download/current/UniProt2Reactome.txt>`_.
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207
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208 -----
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209
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210 .. class:: infomark
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211
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212 **Authors**
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213
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214 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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215
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216 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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217
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218 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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219
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220 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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221
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222 ]]></help>
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223 <citations>
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224 </citations>
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225
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226 </tool>