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comparison InclusionExclusionListCreator.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.0.0">
3 <description>Creates inclusion and/or exclusion lists.</description>
4 <macros>
5 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>InclusionExclusionListCreator
11
12 #if $param_include:
13 -include $param_include
14 #end if
15 #if $param_exclude:
16 -exclude $param_exclude
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_rt_model:
22 -rt_model $param_rt_model
23 #end if
24 #if $param_pt_model:
25 -pt_model $param_pt_model
26 #end if
27
28 #if $rep_param_inclusion_charges:
29 -inclusion_charges
30 #for token in $rep_param_inclusion_charges:
31 #if " " in str(token):
32 "$token.param_inclusion_charges"
33 #else
34 $token.param_inclusion_charges
35 #end if
36 #end for
37 #end if
38 #if $param_inclusion_strategy:
39 -inclusion_strategy
40 #if " " in str($param_inclusion_strategy):
41 "$param_inclusion_strategy"
42 #else
43 $param_inclusion_strategy
44 #end if
45 #end if
46
47 #if $rep_param_exclusion_charges:
48 -exclusion_charges
49 #for token in $rep_param_exclusion_charges:
50 #if " " in str(token):
51 "$token.param_exclusion_charges"
52 #else
53 $token.param_exclusion_charges
54 #end if
55 #end for
56 #end if
57 #if $param_raw_data:
58 -raw_data $param_raw_data
59 #end if
60 -threads \${GALAXY_SLOTS:-24}
61 #if $param_algorithm_InclusionExclusionList_missed_cleavages:
62 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
63 #end if
64 #if $param_algorithm_InclusionExclusionList_RT_unit:
65 -algorithm:InclusionExclusionList:RT:unit
66 #if " " in str($param_algorithm_InclusionExclusionList_RT_unit):
67 "$param_algorithm_InclusionExclusionList_RT_unit"
68 #else
69 $param_algorithm_InclusionExclusionList_RT_unit
70 #end if
71 #end if
72 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
73 -algorithm:InclusionExclusionList:RT:use_relative
74 #end if
75 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
76 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
77 #end if
78 #if $param_algorithm_InclusionExclusionList_RT_window_absolute:
79 -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute
80 #end if
81 #if $param_algorithm_InclusionExclusionList_merge_mz_tol:
82 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
83 #end if
84 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
85 -algorithm:InclusionExclusionList:merge:mz_tol_unit
86 #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
87 "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit"
88 #else
89 $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
90 #end if
91 #end if
92 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
93 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
94 #end if
95 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
96 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin
97 #end if
98 #if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks:
99 -algorithm:PrecursorSelection:exclude_overlapping_peaks
100 #end if
101 #if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion:
102 -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion
103 #end if
104 #if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time:
105 -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time
106 #end if
107 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size:
108 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size
109 #end if
110 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt:
111 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt
112 #end if
113 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt:
114 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt
115 #end if
116 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size:
117 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size
118 #end if
119 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size:
120 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size
121 #end if
122 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability:
123 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability
124 #end if
125 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight:
126 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight
127 #end if
128 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz:
129 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz
130 #end if
131 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz:
132 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz
133 #end if
134 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule:
135 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule
136 #end if
137 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids:
138 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids
139 #end if
140 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability:
141 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability
142 #end if
143 #if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization:
144 -algorithm:PrecursorSelection:feature_based:no_intensity_normalization
145 #end if
146 #if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature:
147 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature
148 #end if
149 #if $adv_opts.adv_opts_selector=='advanced':
150 #if $adv_opts.param_force:
151 -force
152 #end if
153 #end if
154 </command>
155 <inputs>
156 <param name="param_include" type="data" format="fasta,featurexml" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
157 <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) "/>
158 <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) "/>
159 <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) "/>
160 <repeat name="rep_param_inclusion_charges" min="0" title="param_inclusion_charges">
161 <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) ">
162 <sanitizer>
163 <valid initial="string.printable">
164 <remove value="'"/>
165 <remove value="&quot;"/>
166 </valid>
167 </sanitizer>
168 </param>
169 </repeat>
170 <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy) ">
171 <option value="FeatureBased_LP">FeatureBased_LP</option>
172 <option value="ProteinBased_LP">ProteinBased_LP</option>
173 <option value="ALL">ALL</option>
174 </param>
175 <repeat name="rep_param_exclusion_charges" min="0" title="param_exclusion_charges">
176 <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) ">
177 <sanitizer>
178 <valid initial="string.printable">
179 <remove value="'"/>
180 <remove value="&quot;"/>
181 </valid>
182 </sanitizer>
183 </param>
184 </repeat>
185 <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) "/>
186 <param name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion" help="(-missed_cleavages) &lt;br&gt;"/>
187 <param name="param_algorithm_InclusionExclusionList_RT_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit) ">
188 <option value="minutes">minutes</option>
189 <option value="seconds">seconds</option>
190 </param>
191 <param name="param_algorithm_InclusionExclusionList_RT_use_relative" type="boolean" truevalue="-algorithm:InclusionExclusionList:RT:use_relative" falsevalue="" checked="true" optional="True" label="Use relative RT window, which depends on RT of precurso" help="(-use_relative) "/>
192 <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]"/>
193 <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]"/>
194 <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'"/>
195 <param name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit) ">
196 <option value="ppm">ppm</option>
197 <option value="Da">Da</option>
198 </param>
199 <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]"/>
200 <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) "/>
201 <param name="param_algorithm_PrecursorSelection_exclude_overlapping_peaks" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection" help="(-exclude_overlapping_peaks) "/>
202 <param name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" 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) "/>
203 <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) "/>
204 <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) "/>
205 <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) "/>
206 <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) "/>
207 <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) "/>
208 <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) "/>
209 <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) "/>
210 <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) "/>
211 <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) "/>
212 <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) "/>
213 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" 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) "/>
214 <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) "/>
215 <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) "/>
216 <param name="param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization" 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"/>
217 <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) "/>
218 <expand macro="advanced_options">
219 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
220 </expand>
221 </inputs>
222 <outputs>
223 <data name="param_out" format="tabular"/>
224 </outputs>
225 <help>**What it does**
226
227 Creates inclusion and/or exclusion lists.
228
229
230 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help>
231 <expand macro="references"/>
232 </tool>