Mercurial > repos > bgruening > uniprot_rest_interface
comparison uniprot.xml @ 6:054483e27a35 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit f7a71c09b68d85a73a7ce761b4e64d5de29daee0
author | bgruening |
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date | Sun, 16 Sep 2018 13:41:08 -0400 |
parents | fe94765e8814 |
children | bfdc6a7ffd3a |
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5:f7ebd1b4783b | 6:054483e27a35 |
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1 <tool id="uniprot" name="UniProt" version="0.1"> | 1 <tool id="uniprot" name="UniProt" version="0.2"> |
2 <description>ID mapping and retrieval</description> | 2 <description>ID mapping and retrieval</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="2.7">requests</requirement> | 7 <requirement type="package" version="2.19.1">requests</requirement> |
8 </requirements> | 8 </requirements> |
9 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> | 9 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> |
10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
11 | 11 |
12 cut -f ${id_column} $infile > id_file.tabular && | 12 cut -f ${id_column} '$infile' > id_file.tabular && |
13 | 13 |
14 $__tool_directory__/uniprot.py | 14 '$__tool_directory__/uniprot.py' |
15 | 15 |
16 #if $tool.tool_choice == "retrieve": | 16 #if $tool.tool_choice == "retrieve": |
17 retrieve -f $tool.format $infile ./output | 17 retrieve -f $tool.format id_file.tabular ./output |
18 #elif $tool.tool_choice == "map": | 18 #elif $tool.tool_choice == "map": |
19 map | 19 map |
20 | 20 |
21 #if $tool.from.category_FROM == "uniprot" | 21 #if $tool.from.category_FROM == "uniprot" |
22 '${tool.from.db_uniprot_FROM}' | 22 '${tool.from.db_uniprot_FROM}' |