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comparison morpheus.xml @ 2:e0104a9f20f0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 93e02b037bfb37001de2bfb6fc731539c1902e80
author galaxyp
date Thu, 12 Jan 2017 15:50:48 -0500
parents ecb9ec15083d
children 8295d959ca28
comparison
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1:ecb9ec15083d 2:e0104a9f20f0
55 <command><![CDATA[ 55 <command><![CDATA[
56 mkdir -p output_reports && 56 mkdir -p output_reports &&
57 cwd=`pwd` && 57 cwd=`pwd` &&
58 #import re 58 #import re
59 #set $searchdb_name = $searchdb 59 #set $searchdb_name = $searchdb
60 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 60 #if $searchdb.is_of_type('uniprotxml'):
61 #set $searchdb_name = 'searchdb.xml' 61 #set $searchdb_name = 'searchdb.xml'
62 #else 62 #else
63 #set $searchdb_name = 'searchdb.fasta' 63 #set $searchdb_name = 'searchdb.fasta'
64 #end if 64 #end if
65 ln -s $searchdb $searchdb_name 65 ln -s $searchdb $searchdb_name
78 78
79 mono `which morpheus` 79 mono `which morpheus`
80 -d='$input_names' 80 -d='$input_names'
81 -db='$searchdb_name' 81 -db='$searchdb_name'
82 82
83 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 83 #if $searchdb.is_of_type('uniprotxml'):
84 #if str( $advanced.adv_options_selector) == "set": 84 #if str( $advanced.adv_options_selector) == "set":
85 $advanced.noup 85 $advanced.noup
86 #end if 86 #end if
87 #end if 87 #end if
88 ## fm vm fdr mvmi precmt precmtv precmtu 88 ## fm vm fdr mvmi precmt precmtv precmtu