Mercurial > repos > galaxyp > reactome_pathwaymatcher

comparison pathwaymatcher.xml @ 1:5d0c44bc354d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 7e04827e48352f6b28cf2e2c93a89a270e5bf026
author galaxyp
date Wed, 04 Jul 2018 04:28:07 -0400
parents f66af2b04a98
children 9a599f278852
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0:f66af2b04a98 1:5d0c44bc354d
1 <tool id="reactome_pathwaymatcher" name="Pathway Matcher" version="@PATHWAYMATCHER_VERSION@.@TOOL_SUBVERSION@"> 1 <tool id="reactome_pathwaymatcher" name="Pathway Matcher" version="@PATHWAYMATCHER_VERSION@.@TOOL_SUBVERSION@">
2 <description> 2 <description>
3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. 3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@PATHWAYMATCHER_VERSION@">1.8</token> 6 <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
7 <token name="@TOOL_SUBVERSION@">0</token> 7 <token name="@TOOL_SUBVERSION@">0</token>
8 <xml name="input_fasta"> 8 <xml name="input_fasta">
9 <param format="fasta" name="input_database" type="data" label="Protein Database" 9 <param format="fasta" name="input_database" type="data" label="Protein Database"
10 help="Select FASTA database from history"/> 10 help="Select FASTA database from history"/>
11 </xml> 11 </xml>
85 #end if 85 #end if
86 86
87 ## PROTEOFORMS 87 ## PROTEOFORMS
88 88
89 #if $s.input_type.input_type_selector == "proteoforms" 89 #if $s.input_type.input_type_selector == "proteoforms"
90
91 #if $s.input_type.proteoform_match_criteria: 90 #if $s.input_type.proteoform_match_criteria:
92 -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}' 91 -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}'
93 #else: 92 #else:
94 -t proteoform -i '${s.input_type.input_proteoforms}' 93 -t proteoform -i '${s.input_type.input_proteoforms}'
95 #end if 94 #end if
96
97 #end if 95 #end if
98 96
99 #end for 97 #end for
100 98
101 ## OUTPUT OPTIONS 99 ## OUTPUT OPTIONS