Mercurial > repos > proteore > proteore_id_converter

annotate id_converter.xml @ 2:f8564e97ccd9 draft

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author proteore
date Fri, 24 Aug 2018 04:35:33 -0400
parents e4d9a4ab1930
children dbbc5b3ecdc1
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1 <tool id="IDconverter" name="ID Converter" version="2018.08.22">
0
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2 <description>convert public database identifiers
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="3.4.1">R</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command interpreter="Rscript">
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11 $__tool_directory__/id_converter_UniProt.R
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12 --id_type="$species.idtypein"
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13 #if $input.ids == "text"
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14 --input="$input.txt"
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15 --input_type="list"
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16 #else
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17 --input="$input.file"
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18 --column_number="$input.ncol"
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19 --header="$input.header"
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20 --input_type="file"
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21 #end if
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22 --target_ids="$species.idto.idtypeout"
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23 --output="$output"
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24 --ref_file="${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables['id_mapping_file'].get_fields() )[0][-1] }"
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25
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26 </command>
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27 <inputs>
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28 <conditional name="input" >
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29 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
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30 <option value="text">Copy/paste your identifiers</option>
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31 <option value="file" selected="true">Input file containing your identifiers</option>
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32 </param>
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33 <when value="text" >
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34 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
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35 <sanitizer invalid_char="">
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36 <valid initial="string.printable">
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37 <remove value="&apos;"/>
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38 </valid>
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39 <mapping initial="none">
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40 <add source="&apos;" target="__sq__"/>
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41 <add source="&#x20;" target=""/>
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42 <add source="&#xA;" target=""/>
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43 <add source="&#xD;" target=""/>
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44 <add source="&#x9;" target=""/>
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45 </mapping>
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46 </sanitizer>
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47 </param>
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48 </when>
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49 <when value="file" >
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50 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
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51 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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52 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
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53 </when>
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54 </conditional>
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55 <conditional name="species">
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56 <param name="mapping_file" type="select" label="Select species for ID conversion" >
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57 <options from_data_table="id_mapping_file"/>
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58 <option value="human_id_mapping"></option>
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59 <option value="mouse_id_mapping"></option>
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60 </param>
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61 <when value="human_id_mapping">
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62 <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
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63 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
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64 <option value="UniProt.AC" selected="True" >Uniprot accession number (e.g. P31946)</option>
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65 <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
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66 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
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67 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
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68 <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
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69 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
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70 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
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71 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
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72 <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
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73 <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
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74 <option value="Ensembl" >Ensembl gene ID (e.g. ENSG00000166913)</option>
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75 <option value="Ensembl_TRS" >Ensembl transcript ID (e.g. ENST00000353703)</option>
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76 <option value="Ensembl_PRO" >Ensembl protein ID (e.g. ENSP00000300161)</option>
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77 <option value="BioGrid" >BioGrid (e.g. 113361)</option>
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78 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
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79 <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
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80 </param>
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81 <section name="idto" title="Target type of IDs" expanded="True" >
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82 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" help="Please see example of IDs in help section" >
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83 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
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84 <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option>
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85 <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
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86 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
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87 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
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88 <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
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89 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
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90 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
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91 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
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92 <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
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93 <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
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94 <option value="Ensembl" >Ensembl gene ID (e.g. ENSG00000166913)</option>
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95 <option value="Ensembl_TRS" >Ensembl transcript ID (e.g. ENST00000353703)</option>
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96 <option value="Ensembl_PRO" >Ensembl protein ID (e.g. ENSP00000300161)</option>
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97 <option value="BioGrid" >BioGrid (e.g. 113361)</option>
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98 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
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99 <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
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100 </param>
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101 </section>
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102 </when>
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103 <when value="mouse_id_mapping">
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104 <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
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105 <option value="UniProt.AC" selected="True" >Uniprot accession number (e.g. P31946)</option>
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106 <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
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107 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
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108 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
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109 <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
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110 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
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111 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
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112 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
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113 <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
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114 <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
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115 <option value="Ensembl" >Ensembl gene ID (e.g. ENSG00000166913)</option>
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116 <option value="Ensembl_TRS" >Ensembl transcript ID (e.g. ENST00000353703)</option>
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117 <option value="Ensembl_PRO" >Ensembl protein ID (e.g. ENSP00000300161)</option>
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118 <option value="BioGrid" >BioGrid (e.g. 113361)</option>
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119 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
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120 <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
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121 </param>
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122 <section name="idto" title="Target type of IDs" expanded="True" >
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123 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" help="Please see example of IDs in help section" >
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124 <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option>
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125 <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
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126 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
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127 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
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128 <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
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129 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
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130 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
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131 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
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132 <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
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133 <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
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134 <option value="Ensembl" >Ensembl gene ID (e.g. ENSG00000166913)</option>
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135 <option value="Ensembl_TRS" >Ensembl transcript ID (e.g. ENST00000353703)</option>
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136 <option value="Ensembl_PRO" >Ensembl protein ID (e.g. ENSP00000300161)</option>
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137 <option value="BioGrid" >BioGrid (e.g. 113361)</option>
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138 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
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139 <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
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140 </param>
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141 </section>
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142 </when>
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143 </conditional>
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144 </inputs>
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145 <outputs>
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146 <data name="output" format="tabular" />
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147 </outputs>
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148 <tests>
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149 <test>
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150 <conditional name="input" >
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151 <param name="ids" value="file"/>
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152 <param name="file" value="FKW_Lacombe_et_al_2017_OK.txt" />
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153 <param name="header" value="true" />
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154 <param name="ncol" value="c1"/>
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155 </conditional>
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156 <conditional name="species">
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157 <param name="mapping_file" value="human_id_mapping"/>
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158 <param name="idtypein" value="UniProt.AC"/>
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159 <section name="idto">
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160 <param name="idtypeout" value="neXtProt,UniProt.ID,GeneID,MIM,Ensembl" />
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161 </section>
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162 </conditional>
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163 <output name="output" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
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164 </test>
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165 </tests>
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166 <help><![CDATA[
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167 This tool converts a list of IDs to another identifier type, select the source and target type from the dropdown menus above (see below supported source and target types).
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168
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169 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to.
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170
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171 If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. Please, note that a "NA" is returned when there is no corresponding ID.
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172
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173 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
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174
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175 **Available databases**
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176
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177 * neXtProt ID (e.g. NX_P31946)
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178
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179 * Uniprot accession number (e.g. P31946)
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180
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181 * Uniprot ID (e.g 1433B_HUMAN)
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182
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183 * Entrez gene ID (e.g. 7529)
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184
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185 * RefSeq (NCBI) protein (e.g. NP_003395.1)
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186
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187 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)
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188
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189 * Protein DataBank ID (e.g. 2BR9:A)
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190
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191 * GOterms (Gene Ontology) ID (e.g. GO:0070062)
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192
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193 * Protein Information Resource ID (e.g. S34755)
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194
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195 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)
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196
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197 * Unigene ID (e.g. Hs.643544)
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198
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199 * Ensembl gene ID (e.g. ENSG00000166913)
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200
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201 * Ensembl transcript ID (e.g. ENST00000353703)
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202
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203 * Ensembl protein ID (e.g. ENSP00000300161)
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204
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205 -----
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206
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207 .. class:: infomark
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208
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209 This tool converts human IDs using the following source files:
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210
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211 * HUMAN_9606_idmapping_selected.tab (Uniprot 02/07/2018)
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212 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
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213
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214 * HUMAN_9606_idmapping.dat (Uniprot 02/07/18)
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215 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
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216
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217 * nextprot_ac_list_all.txt (Nextprot released on 17/01/2018)
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218 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
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219
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220 -----
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221
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222 .. class:: warningmark
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223
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224 Accession numbers with an hyphen ("-") that normally correspond to isoform are considered
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225 (and will therefore be treated) as similar to its canonical form.
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226
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227 For example, "Q71U36-2" will be treated as "Q71U36".
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228
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229 -----
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230
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231 .. class:: infomark
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232
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233 **Authors**
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234
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235 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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236
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237 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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238
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239 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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240
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241 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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242
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243 ]]></help>
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244 <citations>
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245 </citations>
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246 </tool>