Mercurial > repos > galaxyp > openms_precursorionselector

comparison PrecursorIonSelector.xml @ 1:828f4c70d584 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 09:02:59 -0400
parents 45a9649b4891
children 59e80620e2df
comparison
equal deleted inserted replaced
0:45a9649b4891 1:828f4c70d584
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="PrecursorIonSelector" name="PrecursorIonSelector" version="2.1.0"> 4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.2.0">
5 <description>PrecursorIonSelector</description> 5 <description>PrecursorIonSelector</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PrecursorIonSelector</token> 7 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
61 $token.param_fixed_modifications 61 $token.param_fixed_modifications
62 #end if 62 #end if
63 #end for 63 #end for
64 #end if 64 #end if
65 #if $param_algorithm_type: 65 #if $param_algorithm_type:
66 -algorithm:type $param_algorithm_type 66 -algorithm:type
67 #if " " in str($param_algorithm_type):
68 "$param_algorithm_type"
69 #else
70 $param_algorithm_type
71 #end if
67 #end if 72 #end if
68 #if $param_algorithm_max_iteration: 73 #if $param_algorithm_max_iteration:
69 -algorithm:max_iteration $param_algorithm_max_iteration 74 -algorithm:max_iteration $param_algorithm_max_iteration
70 #end if 75 #end if
71 #if $param_algorithm_rt_bin_capacity: 76 #if $param_algorithm_rt_bin_capacity:
118 #end if 123 #end if
119 #if $param_algorithm_MIPFormulation_combined_ilp_k3: 124 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
120 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3 125 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
121 #end if 126 #end if
122 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs: 127 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
123 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs 128 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
129 #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs):
130 "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs"
131 #else
132 $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
133 #end if
124 #end if 134 #end if
125 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization: 135 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
126 -algorithm:MIPFormulation:feature_based:no_intensity_normalization 136 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
127 #end if 137 #end if
128 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature: 138 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
130 #end if 140 #end if
131 #if $param_algorithm_Preprocessing_precursor_mass_tolerance: 141 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
132 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance 142 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
133 #end if 143 #end if
134 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit: 144 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
135 -algorithm:Preprocessing:precursor_mass_tolerance_unit $param_algorithm_Preprocessing_precursor_mass_tolerance_unit 145 -algorithm:Preprocessing:precursor_mass_tolerance_unit
146 #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
147 "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
148 #else
149 $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
150 #end if
136 #end if 151 #end if
137 #if $param_algorithm_Preprocessing_preprocessed_db_path: 152 #if $param_algorithm_Preprocessing_preprocessed_db_path:
138 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path" 153 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path"
139 #end if 154 #end if
140 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path: 155 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
173 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma: 188 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
174 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma 189 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
175 #end if 190 #end if
176 #if $adv_opts.adv_opts_selector=='advanced': 191 #if $adv_opts.adv_opts_selector=='advanced':
177 #if $adv_opts.param_solver: 192 #if $adv_opts.param_solver:
178 -solver $adv_opts.param_solver 193 -solver
194 #if " " in str($adv_opts.param_solver):
195 "$adv_opts.param_solver"
196 #else
197 $adv_opts.param_solver
198 #end if
179 #end if 199 #end if
180 #if $adv_opts.param_force: 200 #if $adv_opts.param_force:
181 -force 201 -force
182 #end if 202 #end if
183 #end if 203 #end if