Mercurial > repos > galaxyp > openms_inclusionexclusionlistcreator
comparison InclusionExclusionListCreator.xml @ 0:468da161b121 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:27:13 -0500 |
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children | b4e991d49651 |
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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.--> | |
3 <!--Proposed Tool Section: [Targeted Experiments]--> | |
4 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.1.0"> | |
5 <description>Creates inclusion and/or exclusion lists.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>InclusionExclusionListCreator | |
14 | |
15 #if $param_include: | |
16 -include $param_include | |
17 #end if | |
18 #if $param_exclude: | |
19 -exclude $param_exclude | |
20 #end if | |
21 #if $param_out: | |
22 -out $param_out | |
23 #end if | |
24 #if $param_rt_model: | |
25 -rt_model $param_rt_model | |
26 #end if | |
27 #if $param_pt_model: | |
28 -pt_model $param_pt_model | |
29 #end if | |
30 | |
31 #if $rep_param_inclusion_charges: | |
32 -inclusion_charges | |
33 #for token in $rep_param_inclusion_charges: | |
34 #if " " in str(token): | |
35 "$token.param_inclusion_charges" | |
36 #else | |
37 $token.param_inclusion_charges | |
38 #end if | |
39 #end for | |
40 #end if | |
41 #if $param_inclusion_strategy: | |
42 -inclusion_strategy $param_inclusion_strategy | |
43 #end if | |
44 | |
45 #if $rep_param_exclusion_charges: | |
46 -exclusion_charges | |
47 #for token in $rep_param_exclusion_charges: | |
48 #if " " in str(token): | |
49 "$token.param_exclusion_charges" | |
50 #else | |
51 $token.param_exclusion_charges | |
52 #end if | |
53 #end for | |
54 #end if | |
55 #if $param_raw_data: | |
56 -raw_data $param_raw_data | |
57 #end if | |
58 #if $param_algorithm_InclusionExclusionList_missed_cleavages: | |
59 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages | |
60 #end if | |
61 #if $param_algorithm_InclusionExclusionList_RT_unit: | |
62 -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit | |
63 #end if | |
64 #if $param_algorithm_InclusionExclusionList_RT_use_relative: | |
65 -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative | |
66 #end if | |
67 #if $param_algorithm_InclusionExclusionList_RT_window_relative: | |
68 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative | |
69 #end if | |
70 #if $param_algorithm_InclusionExclusionList_RT_window_absolute: | |
71 -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute | |
72 #end if | |
73 #if $param_algorithm_InclusionExclusionList_merge_mz_tol: | |
74 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol | |
75 #end if | |
76 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit: | |
77 -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit | |
78 #end if | |
79 #if $param_algorithm_InclusionExclusionList_merge_rt_tol: | |
80 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol | |
81 #end if | |
82 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin: | |
83 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin | |
84 #end if | |
85 #if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks: | |
86 -algorithm:PrecursorSelection:exclude_overlapping_peaks | |
87 #end if | |
88 #if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion: | |
89 -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion | |
90 #end if | |
91 #if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time: | |
92 -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time | |
93 #end if | |
94 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size: | |
95 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size | |
96 #end if | |
97 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt: | |
98 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt | |
99 #end if | |
100 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt: | |
101 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt | |
102 #end if | |
103 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size: | |
104 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size | |
105 #end if | |
106 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size: | |
107 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size | |
108 #end if | |
109 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability: | |
110 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability | |
111 #end if | |
112 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight: | |
113 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight | |
114 #end if | |
115 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz: | |
116 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz | |
117 #end if | |
118 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz: | |
119 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz | |
120 #end if | |
121 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule: | |
122 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule | |
123 #end if | |
124 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids: | |
125 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids | |
126 #end if | |
127 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability: | |
128 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability | |
129 #end if | |
130 #if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization: | |
131 -algorithm:PrecursorSelection:feature_based:no_intensity_normalization | |
132 #end if | |
133 #if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature: | |
134 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature | |
135 #end if | |
136 #if $adv_opts.adv_opts_selector=='advanced': | |
137 #if $adv_opts.param_force: | |
138 -force | |
139 #end if | |
140 #end if | |
141 </command> | |
142 <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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
147 <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) "> | |
149 <sanitizer> | |
150 <valid initial="string.printable"> | |
151 <remove value="'"/> | |
152 <remove value="""/> | |
153 </valid> | |
154 </sanitizer> | |
155 </param> | |
156 </repeat> | |
157 <param name="param_inclusion_strategy" display="radio" type="select" optional="False" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy) "> | |
158 <option value="FeatureBased_LP">FeatureBased_LP</option> | |
159 <option value="ProteinBased_LP">ProteinBased_LP</option> | |
160 <option value="ALL" selected="true">ALL</option> | |
161 </param> | |
162 <repeat name="rep_param_exclusion_charges" min="0" max="1" title="param_exclusion_charges"> | |
163 <param name="param_exclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated" help="(-exclusion_charges) "> | |
164 <sanitizer> | |
165 <valid initial="string.printable"> | |
166 <remove value="'"/> | |
167 <remove value="""/> | |
168 </valid> | |
169 </sanitizer> | |
170 </param> | |
171 </repeat> | |
172 <param name="param_raw_data" type="data" format="mzml" optional="True" label="File containing the raw data (only needed for FeatureBased_LP)" help="(-raw_data) "/> | |
173 <param name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion" help="(-missed_cleavages) <br>"/> | |
174 <param name="param_algorithm_InclusionExclusionList_RT_unit" display="radio" type="select" optional="False" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit) "> | |
175 <option value="minutes" selected="true">minutes</option> | |
176 <option value="seconds">seconds</option> | |
177 </param> | |
178 <param name="param_algorithm_InclusionExclusionList_RT_use_relative" display="radio" type="select" optional="False" value="true" label="Use relative RT window, which depends on RT of precurso" help="(-use_relative) "> | |
179 <option value="true" selected="true">true</option> | |
180 <option value="false">false</option> | |
181 </param> | |
182 <param name="param_algorithm_InclusionExclusionList_RT_window_relative" type="float" min="0.0" max="10.0" optional="True" value="0.05" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window," help="(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]"/> | |
183 <param name="param_algorithm_InclusionExclusionList_RT_window_absolute" type="float" min="0.0" optional="True" value="90.0" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec]," help="(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]"/> | |
184 <param name="param_algorithm_InclusionExclusionList_merge_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance" help="(-mz_tol) Unit of this is defined in 'mz_tol_unit'"/> | |
185 <param name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit) "> | |
186 <option value="ppm" selected="true">ppm</option> | |
187 <option value="Da">Da</option> | |
188 </param> | |
189 <param name="param_algorithm_InclusionExclusionList_merge_rt_tol" type="float" min="0.0" optional="True" value="1.1" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows)" help="(-rt_tol) Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]"/> | |
190 <param name="param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help="(-ms2_spectra_per_rt_bin) "/> | |
191 <param name="param_algorithm_PrecursorSelection_exclude_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help="(-exclude_overlapping_peaks) "/> | |
192 <param name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion" falsevalue="" checked="false" optional="True" label="If true dynamic exclusion is applied" help="(-use_dynamic_exclusion) "/> | |
193 <param name="param_algorithm_PrecursorSelection_Exclusion_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded" help="(-exclusion_time) "/> | |
194 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list" help="(-max_list_size) "/> | |
195 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds" help="(-min_rt) "/> | |
196 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds" help="(-max_rt) "/> | |
197 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds" help="(-rt_step_size) "/> | |
198 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds" help="(-rt_window_size) "/> | |
199 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/> | |
200 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/> | |
201 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/> | |
202 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/> | |
203 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/> | |
204 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/> | |
205 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/> | |
206 <param name="param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/> | |
207 <param name="param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature" help="(-max_number_precursors_per_feature) "/> | |
208 <expand macro="advanced_options"> | |
209 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
210 </expand> | |
211 </inputs> | |
212 <outputs> | |
213 <data name="param_out" format="tabular"/> | |
214 </outputs> | |
215 <help>Creates inclusion and/or exclusion lists. | |
216 | |
217 | |
218 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help> | |
219 </tool> |