Mercurial > repos > proteore > proteore_id_converter

comparison id_converter.xml @ 18:5252bbcfbdd7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit dc6d9d8f1808c4c6bcc42ac6861a8b811e4cee58-dirty
author proteore
date Fri, 10 May 2019 10:38:46 -0400
parents 1e45ea50f145
children 9d758344d36e
comparison
equal deleted inserted replaced
17:1e45ea50f145 18:5252bbcfbdd7
1 <tool id="IDconverter" name="ID Converter" version="2019.03.07"> 1 <tool id="IDconverter" name="ID Converter" version="2019.05.10">
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>
62 <option value="Mouse" selected="True">Mouse (Mus musculus)</option> 62 <option value="Mouse" selected="True">Mouse (Mus musculus)</option>
63 <option value="Rat" selected="True">Rat (Rattus norvegicus)</option> 63 <option value="Rat" selected="True">Rat (Rattus norvegicus)</option>
64 </param> 64 </param>
65 <when value="Human"> 65 <when value="Human">
66 <param name="mapping_file" type="select" label="Release" > 66 <param name="mapping_file" type="select" label="Release" >
67 <options from_data_table="proteore_id_mapping_Human"/> 67 <options from_data_table="proteore_id_mapping_Human">
68 <filter type="sort_by" column="0"/>
69 </options>
68 </param> 70 </param>
69 <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" >
70 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> 72 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
71 <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>
72 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 74 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
86 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> 88 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
87 </param> 89 </param>
88 <section name="idto" title="Target type" expanded="True" > 90 <section name="idto" title="Target type" expanded="True" >
89 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 91 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
90 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> 92 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
91 <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option> 93 <option value="UniProt-AC_reviewed" >UniProt accession number (e.g. P31946 - reviewed entries only)</option>
94 <option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)</option>
92 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 95 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
93 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 96 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
94 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> 97 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
95 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option> 98 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
96 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option> 99 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
107 </param> 110 </param>
108 </section> 111 </section>
109 </when> 112 </when>
110 <when value="Mouse"> 113 <when value="Mouse">
111 <param name="mapping_file" type="select" label="Release" > 114 <param name="mapping_file" type="select" label="Release" >
112 <options from_data_table="proteore_id_mapping_Mouse"/> 115 <options from_data_table="proteore_id_mapping_Mouse">
116 <filter type="sort_by" column="0"/>
117 </options>
113 </param> 118 </param>
114 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > 119 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
115 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> 120 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
116 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 121 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
117 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 122 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
129 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option> 134 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
130 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> 135 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
131 </param> 136 </param>
132 <section name="idto" title="Target type of IDs" expanded="True" > 137 <section name="idto" title="Target type of IDs" expanded="True" >
133 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 138 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
134 <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option> 139 <option value="UniProt-AC_reviewed" >UniProt accession number (e.g. P31946 - reviewed entries only)</option>
140 <option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)</option>
135 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 141 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
136 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 142 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
137 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> 143 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
138 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option> 144 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
139 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option> 145 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
149 </param> 155 </param>
150 </section> 156 </section>
151 </when> 157 </when>
152 <when value="Rat"> 158 <when value="Rat">
153 <param name="mapping_file" type="select" label="Release" > 159 <param name="mapping_file" type="select" label="Release" >
154 <options from_data_table="proteore_id_mapping_Rat"/> 160 <options from_data_table="proteore_id_mapping_Rat">
161 <filter type="sort_by" column="0"/>
162 </options>
155 </param> 163 </param>
156 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" > 164 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
157 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> 165 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
158 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 166 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
159 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 167 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
171 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option> 179 <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
172 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> 180 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
173 </param> 181 </param>
174 <section name="idto" title="Target type of IDs" expanded="True" > 182 <section name="idto" title="Target type of IDs" expanded="True" >
175 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" > 183 <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
176 <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option> 184 <option value="UniProt-AC_reviewed" >UniProt accession number (e.g. P31946 - reviewed entries only)</option>
185 <option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)</option>
177 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> 186 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
178 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> 187 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
179 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> 188 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option>
180 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option> 189 <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
181 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option> 190 <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
236 **Parameters** 245 **Parameters**
237 Target type of IDs currently supported: 246 Target type of IDs currently supported:
238 247
239 * neXtProt ID (e.g. NX_P31946) 248 * neXtProt ID (e.g. NX_P31946)
240 249
241 * UniProt accession number (e.g. P31946) 250 * UniProt accession number (e.g. P31946 - reviewed entries only)
251
252 * UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)
242 253
243 * UniProt ID (e.g 1433B_HUMAN) 254 * UniProt ID (e.g 1433B_HUMAN)
244 255
245 * Entrez gene ID (e.g. 7529) 256 * Entrez gene ID (e.g. 7529)
246 257
287 298
288 This tool converts human IDs using the following source files: 299 This tool converts human IDs using the following source files:
289 300
290 - **HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 301 - **HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
291 - **HUMAN_9606_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 302 - **HUMAN_9606_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
303 - `Human uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606&format=list>`_.
292 - **nextprot_ac_list_all.txt (Nextprot released on 10/10/2018)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/ 304 - **nextprot_ac_list_all.txt (Nextprot released on 10/10/2018)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/
293 - **MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 305 - **MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
294 - **MOUSE_10090_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 306 - **MOUSE_10090_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
307 - `Mouse uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090&format=list>`_.
295 - **RAT_10116_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 308 - **RAT_10116_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
296 - **RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 309 - **RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
310 - `Rat uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116&format=list>`_.
297 311
298 ----- 312 -----
299 313
300 .. class:: infomark 314 .. class:: infomark
301 315