Mercurial > repos > galaxyp > openms_mapalignerposeclustering

comparison MapAlignerPoseClustering.xml @ 0:c3d8064d43aa draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:18:00 -0400
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children be2c8a814fa6
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-1:000000000000 0:c3d8064d43aa
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0">
5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command detect_errors="aggressive"><![CDATA[
14
15 #import re
16
17 mkdir -p ./results_trafoxml ./results_out &&
18 MapAlignerPoseClustering
19
20 -in
21 #for $infile in $param_in:
22 '$infile'
23 #end for
24
25 -out
26 #for $infile in $param_in:
27 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
28 './results_out/${escaped_element_identifier}.${infile.extension}'
29 #end for
30
31 -trafo_out
32 #for $infile in $param_in:
33 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
34 './results_trafoxml/${escaped_element_identifier}.trafoxml'
35 #end for
36
37 #if $param_reference_file:
38 -reference:file $param_reference_file
39 #end if
40 #if $param_reference_index:
41 -reference:index $param_reference_index
42 #end if
43 #if $param_algorithm_max_num_peaks_considered:
44 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered
45 #end if
46 #if $param_algorithm_superimposer_mz_pair_max_distance:
47 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance
48 #end if
49 #if $param_algorithm_superimposer_num_used_points:
50 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points
51 #end if
52 #if $param_algorithm_superimposer_scaling_bucket_size:
53 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size
54 #end if
55 #if $param_algorithm_superimposer_shift_bucket_size:
56 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size
57 #end if
58 #if $param_algorithm_pairfinder_second_nearest_gap:
59 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap
60 #end if
61 #if $param_algorithm_pairfinder_use_identifications:
62 -algorithm:pairfinder:use_identifications
63 #end if
64 #if $param_algorithm_pairfinder_ignore_charge:
65 -algorithm:pairfinder:ignore_charge
66 #end if
67 #if $param_algorithm_pairfinder_distance_RT_max_difference:
68 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference
69 #end if
70 #if $param_algorithm_pairfinder_distance_MZ_max_difference:
71 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference
72 #end if
73 #if $param_algorithm_pairfinder_distance_MZ_unit:
74 -algorithm:pairfinder:distance_MZ:unit
75 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit):
76 "$param_algorithm_pairfinder_distance_MZ_unit"
77 #else
78 $param_algorithm_pairfinder_distance_MZ_unit
79 #end if
80 #end if
81 #if $adv_opts.adv_opts_selector=='advanced':
82 #if $adv_opts.param_force:
83 -force
84 #end if
85 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
86 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
87 #end if
88 #if $adv_opts.param_algorithm_superimposer_max_shift:
89 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
90 #end if
91 #if $adv_opts.param_algorithm_superimposer_max_scaling:
92 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
93 #end if
94 #if $adv_opts.param_algorithm_superimposer_dump_buckets:
95 -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets"
96 #end if
97 #if $adv_opts.param_algorithm_superimposer_dump_pairs:
98 -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs"
99 #end if
100 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
101 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
102 #end if
103 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
104 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
105 #end if
106 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent:
107 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent
108 #end if
109 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight:
110 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight
111 #end if
112 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent:
113 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent
114 #end if
115 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight:
116 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight
117 #end if
118 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform:
119 -algorithm:pairfinder:distance_intensity:log_transform
120 #if " " in str($adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform):
121 "$adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform"
122 #else
123 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform
124 #end if
125 #end if
126 #end if
127 ]]>
128 </command>
129 <inputs>
130 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/>
131 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
132 <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
133 <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/>
134 <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing"/>
135 <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points) Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1"/>
136 <param name="param_algorithm_superimposer_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
137 <param name="param_algorithm_superimposer_shift_bucket_size" type="float" min="0.0" optional="True" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans"/>
138 <param name="param_algorithm_pairfinder_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/>
139 <param name="param_algorithm_pairfinder_use_identifications" display="radio" type="boolean" truevalue="-algorithm:pairfinder:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/>
140 <param name="param_algorithm_pairfinder_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
141 <param name="param_algorithm_pairfinder_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
142 <param name="param_algorithm_pairfinder_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
143 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
144 <option value="Da" selected="true">Da</option>
145 <option value="ppm">ppm</option>
146 </param>
147 <expand macro="advanced_options">
148 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
149 <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction) "/>
150 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/>
151 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/>
152 <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically">
153 <sanitizer>
154 <valid initial="string.printable">
155 <remove value="'"/>
156 <remove value="&quot;"/>
157 </valid>
158 </sanitizer>
159 </param>
160 <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically">
161 <sanitizer>
162 <valid initial="string.printable">
163 <remove value="'"/>
164 <remove value="&quot;"/>
165 </valid>
166 </sanitizer>
167 </param>
168 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
169 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
170 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
171 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
172 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
173 <param name="param_algorithm_pairfinder_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
174 <param name="param_algorithm_pairfinder_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
175 <option value="enabled">enabled</option>
176 <option value="disabled" selected="true">disabled</option>
177 </param>
178 </expand>
179 </inputs>
180 <outputs>
181 <collection name="out" type="list">
182 <discover_datasets pattern="__designation_and_ext__" directory="results_out"/>
183 </collection>
184
185 <collection name="trafo_out" type="list">
186 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/>
187 </collection>
188 </outputs>
189 <help>Corrects retention time distortions between maps using a pose clustering approach.
190
191 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help>
192 </tool>