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comparison id_converter.xml @ 21:6e65e1c78705 draft default tip

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"planemo upload commit 540dd383c0617193db43bf11457011888751b022-dirty"
author proteore
date Thu, 23 Jan 2020 08:43:51 -0500
parents 77a2cd4162b7
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20:77a2cd4162b7 21:6e65e1c78705
1 <tool id="IDconverter" name="ID Converter" version="2019.06.27"> 1 <tool id="IDconverter" name="ID Converter" version="2020.01.09">
2 <description>(Human, Mouse, Rat) 2 <description>(Human, Mouse, Rat)
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
69 </options> 69 </options>
70 </param> 70 </param>
71 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > 71 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
72 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> 72 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
73 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> 73 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
74 <!--option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed only (e.g. P31946)</option-->
74 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 75 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
75 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 76 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
77 <option value="Gene_Name" >Gene Name (e.g. YWHAB)</option>
76 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> 78 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
77 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option> 79 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
78 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option> 80 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
79 <option value="GO" >GO terms (Gene Ontology) ID (e.g. GO:0070062)</option> 81 <option value="GO" >GO terms (Gene Ontology) ID (e.g. GO:0070062)</option>
80 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option> 82 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
88 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> 90 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
89 </param> 91 </param>
90 <section name="idto" title="Target type" expanded="True" > 92 <section name="idto" title="Target type" expanded="True" >
91 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 93 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
92 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> 94 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
93 <option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed entries only)</option> 95 <option value="UniProt-AC" >UniProt accession number (e.g. P31946) - reviewed and unreviewed entries</option>
94 <!--option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)</option--> 96 <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. P31946) - reviewed entries only</option>
95 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 97 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
96 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 98 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
99 <option value="Gene_Name" >Gene Name (e.g. YWHAB)</option>
97 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> 100 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
98 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option> 101 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
99 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option> 102 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
100 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option> 103 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
101 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option> 104 <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
116 <filter type="sort_by" column="0"/> 119 <filter type="sort_by" column="0"/>
117 </options> 120 </options>
118 </param> 121 </param>
119 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > 122 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
120 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. Q8VC49)</option> 123 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. Q8VC49)</option>
124 <!--option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed entries only (e.g. Q8VC49)</option-->
121 <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option> 125 <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option>
122 <option value="GeneID" >Entrez gene ID (e.g. 217845)</option> 126 <option value="GeneID" >Entrez gene ID (e.g. 217845)</option>
127 <option value="Gene_Name" >Gene Name (e.g. Ifi27l2b)</option>
123 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option> 128 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option>
124 <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option> 129 <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option>
125 <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option> 130 <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option>
126 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option> 131 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option>
127 <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option> 132 <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option>
133 <option value="STRING" >STRING (e.g. 10090.ENSMUSP00000041712)</option> 138 <option value="STRING" >STRING (e.g. 10090.ENSMUSP00000041712)</option>
134 <option value="KEGG" >KEGG gene id (e.g. mmu:217845)</option> 139 <option value="KEGG" >KEGG gene id (e.g. mmu:217845)</option>
135 </param> 140 </param>
136 <section name="idto" title="Target type of IDs" expanded="True" > 141 <section name="idto" title="Target type of IDs" expanded="True" >
137 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 142 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
138 <option value="UniProt-AC" >UniProt accession number (e.g. Q8VC49 - reviewed entries only)</option> 143 <option value="UniProt-AC" >UniProt accession number (e.g. Q8VC49) - reviewed and unreviewed entries</option>
139 <!--option value="UniProt-AC" >UniProt accession number (e.g. Q8VC49 - reviewed and unreviewed entries)</option--> 144 <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. Q8VC49) - reviewed entries only</option>
140 <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option> 145 <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option>
141 <option value="GeneID" >Entrez gene ID (e.g. 217845)</option> 146 <option value="GeneID" >Entrez gene ID (e.g. 217845)</option>
147 <option value="Gene_Name" >Gene Name (e.g. Ifi27l2b)</option>
142 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option> 148 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option>
143 <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option> 149 <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option>
144 <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option> 150 <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option>
145 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option> 151 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option>
146 <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option> 152 <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option>
159 <options from_data_table="proteore_id_mapping_Rat"> 165 <options from_data_table="proteore_id_mapping_Rat">
160 <filter type="sort_by" column="0"/> 166 <filter type="sort_by" column="0"/>
161 </options> 167 </options>
162 </param> 168 </param>
163 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" > 169 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
164 <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7 - reviewed entries only)</option> 170 <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7)</option>
171 <!--option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed entries only (e.g. A0JPJ7</option-->
165 <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option> 172 <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option>
166 <option value="GeneID" >Entrez gene ID (e.g. 296488)</option> 173 <option value="GeneID" >Entrez gene ID (e.g. 296488)</option>
174 <option value="Gene_Name" >Gene Name (e.g. Ola1)</option>
167 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option> 175 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option>
168 <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option> 176 <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option>
169 <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option> 177 <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option>
170 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option> 178 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option>
171 <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option> 179 <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option>
177 <option value="STRING" >STRING (e.g. 10116.ENSRNOP00000054039)</option> 185 <option value="STRING" >STRING (e.g. 10116.ENSRNOP00000054039)</option>
178 <option value="KEGG" >KEGG gene id (e.g. rno:296488)</option> 186 <option value="KEGG" >KEGG gene id (e.g. rno:296488)</option>
179 </param> 187 </param>
180 <section name="idto" title="Target type of IDs" expanded="True" > 188 <section name="idto" title="Target type of IDs" expanded="True" >
181 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 189 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
182 <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7 - reviewed entries only)</option> 190 <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7) - reviewed and unreviewed entries</option>
183 <!--option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7 - reviewed and unreviewed entries)</option--> 191 <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. A0JPJ7) - reviewed entries only</option>
184 <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option> 192 <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option>
185 <option value="GeneID" >Entrez gene ID (e.g. 296488)</option> 193 <option value="GeneID" >Entrez gene ID (e.g. 296488)</option>
194 <option value="Gene_Name" >Gene Name (e.g. Ola1)</option>
186 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option> 195 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option>
187 <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option> 196 <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option>
188 <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option> 197 <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option>
189 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option> 198 <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option>
190 <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option> 199 <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option>
281 290
282 * STRING (e.g. 9606.ENSP00000300161) 291 * STRING (e.g. 9606.ENSP00000300161)
283 292
284 * KEGG gene id (e.g. hsa:7529) 293 * KEGG gene id (e.g. hsa:7529)
285 294
286 .. class:: warningmark
287
288 Nextprot and OMIM only applicable to Human species.
289
290 .. class:: warningmark 295 .. class:: warningmark
291 296
292 For Uniprot-AC and uniprot-ID, only reviewed IDs are considered here, except for release before 08-05-2019 where all uniprot-AC and uniprot-ID (at the time) are considered. 297 Output selection
298
299 - **Nextprot** and **OMIM** only applicable to Human species.
300 - **Uniprot-AC reviewed and unreviewed entries**: All uniprot-AC are considered.
301 - **Uniprot-AC reviewed entries only**: only reviewed IDs are considered here
302
303 .. class:: warningmark
304
305 | Output Ids type needs to be different from input Ids type in order to create a new column of converted ids.
306 | For example, if you choose Entrez Gene ID in input ids type and in output ids type, no result column will be created.
307 | For multiple convertion, only output ids type different from the input ids type will create a column.
293 308
294 ----- 309 -----
295 310
296 **Output** 311 **Output**
297 312
304 319
305 This tool converts human IDs using the following source files: 320 This tool converts human IDs using the following source files:
306 321
307 - Current release of Uniprot, for idmapping_selected.tab and idmapping.dat for Human, Mouse and Rat: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism 322 - Current release of Uniprot, for idmapping_selected.tab and idmapping.dat for Human, Mouse and Rat: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism
308 - All previous release of uniprot can be found here: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/ 323 - All previous release of uniprot can be found here: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/
309 - **nextprot_ac_list_all.txt (Nextprot released on 13/02/2019 - current)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/ 324 - **nextprot_ac_list_all.txt (Nextprot released on 22/08/2019 - current)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/
310 - All previous release of **nextprot_ac_list_all.txt** can be foud here: ftp://ftp.nextprot.org/pub/previous_releases/
311 - `Human uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190605]&format=list>`_.
312 - `Mouse uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190605]&format=list>`_.
313 - `Rat uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190605]&format=list>`_.
314 - `Human uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190508]&format=list>`_.
315 - `Mouse uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190508]&format=list>`_.
316 - `Rat uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190508]&format=list>`_.
317 - `Human uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020181010]&format=list>`_.
318 - `Mouse uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020181010]&format=list>`_.
319 - `Rat uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020181010]&format=list>`_.
320 325
321 ----- 326 -----
322 327
323 .. class:: infomark 328 .. class:: infomark
324 329