Mercurial > repos > galaxyp > openms_inclusionexclusionlistcreator

comparison InclusionExclusionListCreator.xml @ 1:b4e991d49651 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 09:12:37 -0400
parents 468da161b121
children 55b031e4872d
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0:468da161b121 1:b4e991d49651
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.1.0"> 4 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.2.0">
5 <description>Creates inclusion and/or exclusion lists.</description> 5 <description>Creates inclusion and/or exclusion lists.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token> 7 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
37 $token.param_inclusion_charges 37 $token.param_inclusion_charges
38 #end if 38 #end if
39 #end for 39 #end for
40 #end if 40 #end if
41 #if $param_inclusion_strategy: 41 #if $param_inclusion_strategy:
42 -inclusion_strategy $param_inclusion_strategy 42 -inclusion_strategy
43 #if " " in str($param_inclusion_strategy):
44 "$param_inclusion_strategy"
45 #else
46 $param_inclusion_strategy
47 #end if
43 #end if 48 #end if
44 49
45 #if $rep_param_exclusion_charges: 50 #if $rep_param_exclusion_charges:
46 -exclusion_charges 51 -exclusion_charges
47 #for token in $rep_param_exclusion_charges: 52 #for token in $rep_param_exclusion_charges:
57 #end if 62 #end if
58 #if $param_algorithm_InclusionExclusionList_missed_cleavages: 63 #if $param_algorithm_InclusionExclusionList_missed_cleavages:
59 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages 64 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
60 #end if 65 #end if
61 #if $param_algorithm_InclusionExclusionList_RT_unit: 66 #if $param_algorithm_InclusionExclusionList_RT_unit:
62 -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit 67 -algorithm:InclusionExclusionList:RT:unit
68 #if " " in str($param_algorithm_InclusionExclusionList_RT_unit):
69 "$param_algorithm_InclusionExclusionList_RT_unit"
70 #else
71 $param_algorithm_InclusionExclusionList_RT_unit
72 #end if
63 #end if 73 #end if
64 #if $param_algorithm_InclusionExclusionList_RT_use_relative: 74 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
65 -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative 75 -algorithm:InclusionExclusionList:RT:use_relative
76 #if " " in str($param_algorithm_InclusionExclusionList_RT_use_relative):
77 "$param_algorithm_InclusionExclusionList_RT_use_relative"
78 #else
79 $param_algorithm_InclusionExclusionList_RT_use_relative
80 #end if
66 #end if 81 #end if
67 #if $param_algorithm_InclusionExclusionList_RT_window_relative: 82 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
68 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative 83 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
69 #end if 84 #end if
70 #if $param_algorithm_InclusionExclusionList_RT_window_absolute: 85 #if $param_algorithm_InclusionExclusionList_RT_window_absolute:
72 #end if 87 #end if
73 #if $param_algorithm_InclusionExclusionList_merge_mz_tol: 88 #if $param_algorithm_InclusionExclusionList_merge_mz_tol:
74 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol 89 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
75 #end if 90 #end if
76 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit: 91 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
77 -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit 92 -algorithm:InclusionExclusionList:merge:mz_tol_unit
93 #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
94 "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit"
95 #else
96 $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
97 #end if
78 #end if 98 #end if
79 #if $param_algorithm_InclusionExclusionList_merge_rt_tol: 99 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
80 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol 100 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
81 #end if 101 #end if
82 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin: 102 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
138 -force 158 -force
139 #end if 159 #end if
140 #end if 160 #end if
141 </command> 161 </command>
142 <inputs> 162 <inputs>
143 <param name="param_include" type="data" format="fasta,featurexml" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/> 163 <param name="param_include" type="data" format="featurexml,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
144 <param name="param_exclude" type="data" format="fasta,featurexml,idxml" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/> 164 <param name="param_exclude" type="data" format="featurexml,idxml,fasta" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/>
145 <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files" help="(-rt_model) "/> 165 <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files" help="(-rt_model) "/>
146 <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" help="(-pt_model) "/> 166 <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" help="(-pt_model) "/>
147 <repeat name="rep_param_inclusion_charges" min="0" max="1" title="param_inclusion_charges"> 167 <repeat name="rep_param_inclusion_charges" min="0" max="1" title="param_inclusion_charges">
148 <param name="param_inclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated" help="(-inclusion_charges) "> 168 <param name="param_inclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated" help="(-inclusion_charges) ">
149 <sanitizer> 169 <sanitizer>