Mercurial > repos > galaxyp > openms_mapalignerposeclustering

comparison MapAlignerPoseClustering.xml @ 0:70f729e59244 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 18:08:16 -0500
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children 40ca4302e603
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-1:000000000000 0:70f729e59244
1 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0">
2 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
3 <macros>
4 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="stdio"/>
8 <expand macro="requirements"/>
9 <command><![CDATA[
10 MapAlignerPoseClustering
11 -in $param_in
12 -out $out
13 -trafo_out $trafo_out
14
15 -threads "\${GALAXY_SLOTS:-1}"
16
17 #if $param_reference_file:
18 -reference:file $param_reference_file
19 #end if
20 #if $param_reference_index:
21 -reference:index $param_reference_index
22 #end if
23 #if $param_algorithm_max_num_peaks_considered:
24 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered
25 #end if
26 #if $param_algorithm_superimposer_mz_pair_max_distance:
27 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance
28 #end if
29 #if $param_algorithm_superimposer_num_used_points:
30 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points
31 #end if
32 #if $param_algorithm_superimposer_scaling_bucket_size:
33 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size
34 #end if
35 #if $param_algorithm_superimposer_shift_bucket_size:
36 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size
37 #end if
38 #if $param_algorithm_pairfinder_second_nearest_gap:
39 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap
40 #end if
41 #if $param_algorithm_pairfinder_use_identifications:
42 -algorithm:pairfinder:use_identifications
43 #end if
44 #if $param_algorithm_pairfinder_ignore_charge:
45 -algorithm:pairfinder:ignore_charge
46 #end if
47 #if $param_algorithm_pairfinder_distance_RT_max_difference:
48 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference
49 #end if
50 #if $param_algorithm_pairfinder_distance_MZ_max_difference:
51 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference
52 #end if
53 #if $param_algorithm_pairfinder_distance_MZ_unit:
54 -algorithm:pairfinder:distance_MZ:unit
55 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit):
56 "$param_algorithm_pairfinder_distance_MZ_unit"
57 #else
58 $param_algorithm_pairfinder_distance_MZ_unit
59 #end if
60 #end if
61 #if $adv_opts.adv_opts_selector=='advanced':
62
63 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
64 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
65 #end if
66 #if $adv_opts.param_algorithm_superimposer_max_shift:
67 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
68 #end if
69 #if $adv_opts.param_algorithm_superimposer_max_scaling:
70 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
71 #end if
72
73 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
74 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
75 #end if
76 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
77 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
78 #end if
79 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent:
80 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent
81 #end if
82 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight:
83 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight
84 #end if
85 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent:
86 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent
87 #end if
88 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight:
89 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight
90 #end if
91 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform:
92 -algorithm:pairfinder:distance_intensity:log_transform
93 #if " " in str($adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform):
94 "$adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform"
95 #else
96 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform
97 #end if
98 #end if
99 #end if
100 ]]>
101 </command>
102 <inputs>
103 <param name="param_in" type="data" format="mzML,featureXML" label="Input files to align (all must have the same file type)" help="(-in) "/>
104 <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) "/>
105 <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"/>
106 <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'"/>
107 <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"/>
108 <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"/>
109 <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"/>
110 <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"/>
111 <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) "/>
112 <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) "/>
113 <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) "/>
114 <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) "/>
115 <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) "/>
116 <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) ">
117 <option value="Da" selected="true">Da</option>
118 <option value="ppm">ppm</option>
119 </param>
120 <expand macro="advanced_options">
121 <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) "/>
122 <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"/>
123 <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"/>
124 <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) "/>
125 <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) "/>
126 <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) "/>
127 <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) "/>
128 <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) "/>
129 <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) "/>
130 <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))">
131 <option value="enabled">enabled</option>
132 <option value="disabled" selected="true">disabled</option>
133 </param>
134 </expand>
135 </inputs>
136 <outputs>
137 <data name="out" format_source="param_in" metadata_source="param_in" />
138 <data name="trafo_out" format_source="param_in" metadata_source="param_in" />
139 </outputs>
140 <help>Corrects retention time distortions between maps using a pose clustering approach.
141
142
143 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
144 </tool>