Mercurial > repos > proteore > proteore_id_converter
comparison id_converter.xml @ 17:1e45ea50f145 draft
planemo upload commit 640429adac783e2354f5caf12d7b6b81b8ddf54f-dirty
| author | proteore |
|---|---|
| date | Thu, 07 Mar 2019 07:49:18 -0500 |
| parents | b6607b7e683f |
| children | 5252bbcfbdd7 |
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| 16:b6607b7e683f | 17:1e45ea50f145 |
|---|---|
| 1 <tool id="IDconverter" name="ID Converter" version="2019.01.28"> | 1 <tool id="IDconverter" name="ID Converter" version="2019.03.07"> |
| 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> |
| 18 --header="$input.header" | 18 --header="$input.header" |
| 19 --input_type="file" | 19 --input_type="file" |
| 20 #end if | 20 #end if |
| 21 --target_ids="$species.idto.idtypeout" | 21 --target_ids="$species.idto.idtypeout" |
| 22 --output="$output" | 22 --output="$output" |
| 23 --ref_file="$__tool_directory__/${ filter( lambda x: str( x[2] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }" | 23 #if "id_mapping" in str($species.mapping_file).split("/") |
| 24 | 24 --ref_file="$species.mapping_file" |
| 25 #else | |
| 26 --ref_file="$__tool_directory__/$species.mapping_file" | |
| 27 #end if | |
| 25 ]]></command> | 28 ]]></command> |
| 26 <inputs> | 29 <inputs> |
| 27 <conditional name="input" > | 30 <conditional name="input" > |
| 28 <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" > | 31 <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" > |
| 29 <option value="text">Copy/paste your identifiers</option> | 32 <option value="text">Copy/paste your identifiers</option> |
| 46 </param> | 49 </param> |
| 47 </when> | 50 </when> |
| 48 <when value="file" > | 51 <when value="file" > |
| 49 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> | 52 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> |
| 50 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> | 53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
| 51 <param name="ncol" type="text" value="c1" label="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' /> | 54 <param name="ncol" type="text" value="c1" label="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'> |
| 55 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
| 56 </param> | |
| 52 </when> | 57 </when> |
| 53 </conditional> | 58 </conditional> |
| 54 <conditional name="species"> | 59 <conditional name="species"> |
| 55 <param name="mapping_file" type="select" label="Species" > | 60 <param name="species" type="select" label="Species"> |
| 56 <options from_data_table="proteore_id_mapping"/> | 61 <option value="Human" selected="True">Human (Homo sapiens)</option> |
| 57 <option value="Human"></option> | 62 <option value="Mouse" selected="True">Mouse (Mus musculus)</option> |
| 58 <option value="Mouse"></option> | 63 <option value="Rat" selected="True">Rat (Rattus norvegicus)</option> |
| 59 <option value="Rat"></option> | |
| 60 </param> | 64 </param> |
| 61 <when value="Human"> | 65 <when value="Human"> |
| 66 <param name="mapping_file" type="select" label="Release" > | |
| 67 <options from_data_table="proteore_id_mapping_Human"/> | |
| 68 </param> | |
| 62 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > | 69 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > |
| 63 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> | 70 <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> |
| 64 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> | 71 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> |
| 65 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> | 72 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> |
| 66 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> | 73 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> |
| 99 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> | 106 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> |
| 100 </param> | 107 </param> |
| 101 </section> | 108 </section> |
| 102 </when> | 109 </when> |
| 103 <when value="Mouse"> | 110 <when value="Mouse"> |
| 111 <param name="mapping_file" type="select" label="Release" > | |
| 112 <options from_data_table="proteore_id_mapping_Mouse"/> | |
| 113 </param> | |
| 104 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > | 114 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > |
| 105 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> | 115 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> |
| 106 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> | 116 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> |
| 107 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> | 117 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> |
| 108 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> | 118 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> |
| 138 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> | 148 <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option> |
| 139 </param> | 149 </param> |
| 140 </section> | 150 </section> |
| 141 </when> | 151 </when> |
| 142 <when value="Rat"> | 152 <when value="Rat"> |
| 153 <param name="mapping_file" type="select" label="Release" > | |
| 154 <options from_data_table="proteore_id_mapping_Rat"/> | |
| 155 </param> | |
| 143 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" > | 156 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" > |
| 144 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> | 157 <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option> |
| 145 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> | 158 <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> |
| 146 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> | 159 <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> |
| 147 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> | 160 <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_003395.1)</option> |