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comparison MascotAdapter.xml @ 1:36da1e3613ea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:22:57 -0400
parents ec7b8772f4c9
children b0fcab295c60
comparison
equal deleted inserted replaced
0:ec7b8772f4c9 1:36da1e3613ea
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="MascotAdapter" name="MascotAdapter" version="2.1.0"> 4 <tool id="MascotAdapter" name="MascotAdapter" version="2.2.0.1">
5 <description>Annotates MS/MS spectra using Mascot.</description> 5 <description>Annotates MS/MS spectra using Mascot.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MascotAdapter</token> 7 <token name="@EXECUTABLE@">MascotAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
32 #end if 32 #end if
33 #if $param_peak_mass_tolerance: 33 #if $param_peak_mass_tolerance:
34 -peak_mass_tolerance $param_peak_mass_tolerance 34 -peak_mass_tolerance $param_peak_mass_tolerance
35 #end if 35 #end if
36 #if $param_taxonomy: 36 #if $param_taxonomy:
37 -taxonomy $param_taxonomy 37 -taxonomy
38 #if " " in str($param_taxonomy):
39 "$param_taxonomy"
40 #else
41 $param_taxonomy
42 #end if
38 #end if 43 #end if
39 44
40 #if $rep_param_modifications: 45 #if $rep_param_modifications:
41 -modifications 46 -modifications
42 #for token in $rep_param_modifications: 47 #for token in $rep_param_modifications:
74 #end if 79 #end if
75 #if $param_hits: 80 #if $param_hits:
76 -hits "$param_hits" 81 -hits "$param_hits"
77 #end if 82 #end if
78 #if $param_cleavage: 83 #if $param_cleavage:
79 -cleavage $param_cleavage 84 -cleavage
85 #if " " in str($param_cleavage):
86 "$param_cleavage"
87 #else
88 $param_cleavage
89 #end if
80 #end if 90 #end if
81 #if $param_missed_cleavages: 91 #if $param_missed_cleavages:
82 -missed_cleavages $param_missed_cleavages 92 -missed_cleavages $param_missed_cleavages
83 #end if 93 #end if
84 #if $param_sig_threshold: 94 #if $param_sig_threshold:
110 #end if 120 #end if
111 #if $param_boundary: 121 #if $param_boundary:
112 -boundary "$param_boundary" 122 -boundary "$param_boundary"
113 #end if 123 #end if
114 #if $param_mass_type: 124 #if $param_mass_type:
115 -mass_type $param_mass_type 125 -mass_type
126 #if " " in str($param_mass_type):
127 "$param_mass_type"
128 #else
129 $param_mass_type
130 #end if
116 #end if 131 #end if
117 #if $param_mascot_directory: 132 #if $param_mascot_directory:
118 -mascot_directory "$param_mascot_directory" 133 -mascot_directory "$param_mascot_directory"
119 #end if 134 #end if
120 #if $param_temp_data_directory: 135 #if $param_temp_data_directory:
125 -force 140 -force
126 #end if 141 #end if
127 #end if 142 #end if
128 </command> 143 </command>
129 <inputs> 144 <inputs>
130 <param name="param_in" type="data" format="text" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/> 145 <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
131 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/> 146 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
132 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/> 147 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
133 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) "> 148 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">
134 <sanitizer> 149 <sanitizer>
135 <valid initial="string.printable"> 150 <valid initial="string.printable">