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comparison MapAlignerIdentification.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
3 <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
4 <macros>
5 <token name="@EXECUTABLE@">MapAlignerIdentification</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>MapAlignerIdentification
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16
17 #if $rep_param_out:
18 -out
19 #for token in $rep_param_out:
20 #if " " in str(token):
21 "$token.param_out"
22 #else
23 $token.param_out
24 #end if
25 #end for
26 #end if
27
28 #if $rep_param_trafo_out:
29 -trafo_out
30 #for token in $rep_param_trafo_out:
31 #if " " in str(token):
32 "$token.param_trafo_out"
33 #else
34 $token.param_trafo_out
35 #end if
36 #end for
37 #end if
38 -threads \${GALAXY_SLOTS:-24}
39 #if $param_reference_file:
40 -reference:file $param_reference_file
41 #end if
42 #if $param_reference_index:
43 -reference:index $param_reference_index
44 #end if
45 #if $param_algorithm_peptide_score_threshold:
46 -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
47 #end if
48 #if $param_algorithm_min_run_occur:
49 -algorithm:min_run_occur $param_algorithm_min_run_occur
50 #end if
51 #if $param_algorithm_max_rt_shift:
52 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
53 #end if
54 #if $param_algorithm_use_unassigned_peptides:
55 -algorithm:use_unassigned_peptides
56 #end if
57 #if $param_algorithm_use_feature_rt:
58 -algorithm:use_feature_rt
59 #end if
60 #if $param_model_type:
61 -model:type
62 #if " " in str($param_model_type):
63 "$param_model_type"
64 #else
65 $param_model_type
66 #end if
67 #end if
68 #if $param_model_linear_symmetric_regression:
69 -model:linear:symmetric_regression
70 #end if
71 #if $param_model_b_spline_wavelength:
72 -model:b_spline:wavelength $param_model_b_spline_wavelength
73 #end if
74 #if $param_model_b_spline_num_nodes:
75 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
76 #end if
77 #if $param_model_b_spline_extrapolate:
78 -model:b_spline:extrapolate
79 #if " " in str($param_model_b_spline_extrapolate):
80 "$param_model_b_spline_extrapolate"
81 #else
82 $param_model_b_spline_extrapolate
83 #end if
84 #end if
85 #if $param_model_b_spline_boundary_condition:
86 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
87 #end if
88 #if $param_model_interpolated_interpolation_type:
89 -model:interpolated:interpolation_type
90 #if " " in str($param_model_interpolated_interpolation_type):
91 "$param_model_interpolated_interpolation_type"
92 #else
93 $param_model_interpolated_interpolation_type
94 #end if
95 #end if
96 #if $adv_opts.adv_opts_selector=='advanced':
97 #if $adv_opts.param_force:
98 -force
99 #end if
100 #end if
101 </command>
102 <inputs>
103 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks (all must have the same file type)" help="(-in) ">
104 <sanitizer>
105 <valid initial="string.printable">
106 <remove value="'"/>
107 <remove value="&quot;"/>
108 </valid>
109 </sanitizer>
110 </param>
111 <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
112 <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"/>
113 <param name="param_algorithm_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment" help="(-peptide_score_threshold) &lt;br&gt;Select a value that allows only 'high confidence' matches"/>
114 <param name="param_algorithm_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl" help="(-min_run_occur) reference, if any) a peptide must occur in to be used for the alignment. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
115 <param name="param_algorithm_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. &lt;br&gt;If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
116 <param name="param_algorithm_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides" falsevalue="" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used"/>
117 <param name="param_algorithm_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" checked="false" optional="True" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. &lt;br&gt;Precludes 'use_unassigned_peptides'"/>
118 <param name="param_model_type" type="select" optional="True" value="b_spline" label="Type of model" help="(-type) ">
119 <option value="linear">linear</option>
120 <option value="b_spline">b_spline</option>
121 <option value="interpolated">interpolated</option>
122 </param>
123 <param name="param_model_linear_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
124 <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
125 <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
126 <param name="param_model_b_spline_extrapolate" type="select" optional="True" value="linear" label="Method to use for extrapolation beyond the original data range" help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
127 <option value="linear">linear</option>
128 <option value="b_spline">b_spline</option>
129 <option value="constant">constant</option>
130 <option value="global_linear">global_linear</option>
131 </param>
132 <param name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/>
133 <param name="param_model_interpolated_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
134 <option value="linear">linear</option>
135 <option value="cspline">cspline</option>
136 <option value="akima">akima</option>
137 </param>
138 <expand macro="advanced_options">
139 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
140 </expand>
141 </inputs>
142 <outputs>
143 <data name="param_out" metadata_source="param_in" format="input"/>
144 <data name="param_trafo_out" format="trafoxml"/>
145 </outputs>
146 <help>**What it does**
147
148 Corrects retention time distortions between maps based on common peptide identifications.
149
150
151 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
152 <expand macro="references"/>
153 </tool>