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comparison MapAlignerIdentification.xml @ 4:bf50f9eb1dcb draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 19:44:14 +0000
parents 1f0a9c3cb526
children 992bb7e5bf8d
comparison
equal deleted inserted replaced
3:ce546b0bf9c2 4:bf50f9eb1dcb
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.3.0"> 4 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description> 5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapAlignerIdentification</token> 7 <token name="@EXECUTABLE@">MapAlignerIdentification</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MapAlignerIdentification 15 @EXT_FOO@
14 16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out &&
23 #end if
24 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir trafo_out &&
26 #end if
27 #if $design:
28 mkdir design &&
29 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
30 #end if
31 #if $reference.file:
32 mkdir reference.file &&
33 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
34 #end if
35
36 ## Main program call
37
38 set -o pipefail &&
39 @EXECUTABLE@ -write_ctd ./ &&
40 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
41 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 42 -in
16 #for token in $param_in: 43 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 44 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
18 #end for 45 -out
19 46 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
20 #if $rep_param_out: 47 #end if
21 -out 48 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 #for token in $rep_param_out: 49 -trafo_out
23 #if " " in str(token): 50 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
24 "$token.param_out" 51 #end if
25 #else 52 #if $design:
26 $token.param_out 53 -design
27 #end if 54 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
28 #end for 55 #end if
29 #end if 56 #if $reference.file:
30 57 -reference:file
31 #if $rep_param_trafo_out: 58 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
32 -trafo_out 59 #end if
33 #for token in $rep_param_trafo_out: 60 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
34 #if " " in str(token): 61 | tee '$stdout'
35 "$token.param_trafo_out" 62 #end if
36 #else 63
37 $token.param_trafo_out 64 ## Postprocessing
38 #end if 65 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
39 #end for 66 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
40 #end if 67 #end if
41 #if $param_design: 68 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
42 -design $param_design 69 && mv '@EXECUTABLE@.ctd' '$ctd_out'
43 #end if 70 #end if]]></command>
44 #if $param_reference_file: 71 <configfiles>
45 -reference:file $param_reference_file 72 <inputs name="args_json" data_style="paths"/>
46 #end if 73 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
47 #if $param_reference_index: 74 </configfiles>
48 -reference:index $param_reference_index
49 #end if
50 #if $param_algorithm_min_run_occur:
51 -algorithm:min_run_occur $param_algorithm_min_run_occur
52 #end if
53 #if $param_algorithm_max_rt_shift:
54 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
55 #end if
56 #if $param_algorithm_use_unassigned_peptides:
57 -algorithm:use_unassigned_peptides
58 #if " " in str($param_algorithm_use_unassigned_peptides):
59 "$param_algorithm_use_unassigned_peptides"
60 #else
61 $param_algorithm_use_unassigned_peptides
62 #end if
63 #end if
64 #if $param_algorithm_use_feature_rt:
65 -algorithm:use_feature_rt
66 #end if
67 #if $param_model_type:
68 -model:type
69 #if " " in str($param_model_type):
70 "$param_model_type"
71 #else
72 $param_model_type
73 #end if
74 #end if
75 #if $param_model_linear_symmetric_regression:
76 -model:linear:symmetric_regression
77 #end if
78 #if $param_model_b_spline_wavelength:
79 -model:b_spline:wavelength $param_model_b_spline_wavelength
80 #end if
81 #if $param_model_b_spline_num_nodes:
82 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
83 #end if
84 #if $param_model_b_spline_extrapolate:
85 -model:b_spline:extrapolate
86 #if " " in str($param_model_b_spline_extrapolate):
87 "$param_model_b_spline_extrapolate"
88 #else
89 $param_model_b_spline_extrapolate
90 #end if
91 #end if
92 #if $param_model_b_spline_boundary_condition:
93 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
94 #end if
95 #if $param_model_lowess_span:
96 -model:lowess:span $param_model_lowess_span
97 #end if
98 #if $param_model_lowess_num_iterations:
99 -model:lowess:num_iterations $param_model_lowess_num_iterations
100 #end if
101 #if $param_model_lowess_delta:
102 -model:lowess:delta $param_model_lowess_delta
103 #end if
104 #if $param_model_lowess_interpolation_type:
105 -model:lowess:interpolation_type
106 #if " " in str($param_model_lowess_interpolation_type):
107 "$param_model_lowess_interpolation_type"
108 #else
109 $param_model_lowess_interpolation_type
110 #end if
111 #end if
112 #if $param_model_lowess_extrapolation_type:
113 -model:lowess:extrapolation_type
114 #if " " in str($param_model_lowess_extrapolation_type):
115 "$param_model_lowess_extrapolation_type"
116 #else
117 $param_model_lowess_extrapolation_type
118 #end if
119 #end if
120 #if $param_model_interpolated_interpolation_type:
121 -model:interpolated:interpolation_type
122 #if " " in str($param_model_interpolated_interpolation_type):
123 "$param_model_interpolated_interpolation_type"
124 #else
125 $param_model_interpolated_interpolation_type
126 #end if
127 #end if
128 #if $param_model_interpolated_extrapolation_type:
129 -model:interpolated:extrapolation_type
130 #if " " in str($param_model_interpolated_extrapolation_type):
131 "$param_model_interpolated_extrapolation_type"
132 #else
133 $param_model_interpolated_extrapolation_type
134 #end if
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> 75 <inputs>
143 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files to align (all must have the same file type)" help="(-in) "> 76 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml data sets(s)"/>
144 <sanitizer> 77 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
145 <valid initial="string.printable"> 78 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
146 <remove value="'"/> 79 <param name="file" argument="-reference:file" type="data" format="consensusxml,featurexml,idxml" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml data sets(s)"/>
147 <remove value="&quot;"/> 80 <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
148 </valid> 81 </section>
149 </sanitizer> 82 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
83 <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If only IDs above a score cutoff should be used" help="Used together with min_score"/>
84 <param name="min_score" argument="-algorithm:min_score" type="float" optional="true" value="0.05" label="Minimum score for an ID to be considered" help="Applies to the last score calculated.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
85 <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" optional="true" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
86 <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" optional="true" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. 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"/>
87 <param name="use_unassigned_peptides" argument="-algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
88 <param name="use_feature_rt" argument="-algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When aligning feature or consensus 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="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
89 </section>
90 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
91 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
92 <option value="linear">linear</option>
93 <option value="b_spline" selected="true">b_spline</option>
94 <option value="lowess">lowess</option>
95 <option value="interpolated">interpolated</option>
96 <expand macro="list_string_san"/>
97 </param>
98 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
99 <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
100 <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help="">
101 <option value="">default (nothing chosen)</option>
102 <option value="1/x">1/x</option>
103 <option value="1/x2">1/x2</option>
104 <option value="ln(x)">ln(x)</option>
105 <option value=""></option>
106 <expand macro="list_string_san"/>
107 </param>
108 <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help="">
109 <option value="">default (nothing chosen)</option>
110 <option value="1/y">1/y</option>
111 <option value="1/y2">1/y2</option>
112 <option value="ln(y)">ln(y)</option>
113 <option value=""></option>
114 <expand macro="list_string_san"/>
115 </param>
116 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
117 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
118 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
119 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
120 </section>
121 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
122 <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="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"/>
123 <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
124 <param name="extrapolate" argument="-model:b_spline:extrapolate" display="radio" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'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)">
125 <option value="linear" selected="true">linear</option>
126 <option value="b_spline">b_spline</option>
127 <option value="constant">constant</option>
128 <option value="global_linear">global_linear</option>
129 <expand macro="list_string_san"/>
130 </param>
131 <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
132 </section>
133 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
134 <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
135 <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
136 <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
137 <param name="interpolation_type" argument="-model:lowess:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
138 <option value="linear">linear</option>
139 <option value="cspline" selected="true">cspline</option>
140 <option value="akima">akima</option>
141 <expand macro="list_string_san"/>
142 </param>
143 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
144 <option value="two-point-linear">two-point-linear</option>
145 <option value="four-point-linear" selected="true">four-point-linear</option>
146 <option value="global-linear">global-linear</option>
147 <expand macro="list_string_san"/>
148 </param>
149 </section>
150 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
151 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help="">
152 <option value="linear">linear</option>
153 <option value="cspline" selected="true">cspline</option>
154 <option value="akima">akima</option>
155 <expand macro="list_string_san"/>
156 </param>
157 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" display="radio" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
158 <option value="two-point-linear" selected="true">two-point-linear</option>
159 <option value="four-point-linear">four-point-linear</option>
160 <option value="global-linear">global-linear</option>
161 <expand macro="list_string_san"/>
162 </param>
163 </section>
164 </section>
165 <expand macro="adv_opts_macro">
166 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
167 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
168 <expand macro="list_string_san"/>
169 </param>
170 </expand>
171 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
172 <option value="out_FLAG">out (Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model)</option>
173 <option value="trafo_out_FLAG">trafo_out (Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model)</option>
174 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
150 </param> 175 </param>
151 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
152 <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference" help="(-file) "/>
153 <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"/>
154 <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) in which a peptide must occur 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"/>
155 <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"/>
156 <param name="param_algorithm_use_unassigned_peptides" display="radio" type="select" optional="False" value="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used">
157 <option value="true" selected="true">true</option>
158 <option value="false">false</option>
159 </param>
160 <param name="param_algorithm_use_feature_rt" display="radio" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" checked="false" optional="True" label="When aligning feature or consensus 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'"/>
161 <param name="param_model_type" display="radio" type="select" optional="False" value="b_spline" label="Type of model" help="(-type) ">
162 <option value="linear">linear</option>
163 <option value="b_spline" selected="true">b_spline</option>
164 <option value="lowess">lowess</option>
165 <option value="interpolated">interpolated</option>
166 </param>
167 <param name="param_model_linear_symmetric_regression" display="radio" 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'"/>
168 <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"/>
169 <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"/>
170 <param name="param_model_b_spline_extrapolate" display="radio" type="select" optional="False" 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)">
171 <option value="linear" selected="true">linear</option>
172 <option value="b_spline">b_spline</option>
173 <option value="constant">constant</option>
174 <option value="global_linear">global_linear</option>
175 </param>
176 <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) "/>
177 <param name="param_model_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="(-span) Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
178 <param name="param_model_lowess_num_iterations" type="integer" min="0" optional="True" value="3" label="Number of robustifying iterations for lowess fitting" help="(-num_iterations) "/>
179 <param name="param_model_lowess_delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input," help="(-delta) e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
180 <param name="param_model_lowess_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Method to use for interpolation between datapoints computed by lowess" help="(-interpolation_type) 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
181 <option value="linear">linear</option>
182 <option value="cspline" selected="true">cspline</option>
183 <option value="akima">akima</option>
184 </param>
185 <param name="param_model_lowess_extrapolation_type" display="radio" type="select" optional="False" value="four-point-linear" label="Method to use for extrapolation outside the data range" help="(-extrapolation_type) 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
186 <option value="two-point-linear">two-point-linear</option>
187 <option value="four-point-linear" selected="true">four-point-linear</option>
188 <option value="global-linear">global-linear</option>
189 </param>
190 <param name="param_model_interpolated_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
191 <option value="linear">linear</option>
192 <option value="cspline" selected="true">cspline</option>
193 <option value="akima">akima</option>
194 </param>
195 <param name="param_model_interpolated_extrapolation_type" display="radio" type="select" optional="False" value="two-point-linear" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="(-extrapolation_type) Note that global-linear may not be continuous at the border">
196 <option value="two-point-linear" selected="true">two-point-linear</option>
197 <option value="four-point-linear">four-point-linear</option>
198 <option value="global-linear">global-linear</option>
199 </param>
200 <expand macro="advanced_options">
201 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
202 </expand>
203 </inputs> 176 </inputs>
204 <outputs> 177 <outputs>
205 <data name="param_out" metadata_source="param_in" format="input"/> 178 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
206 <data name="param_trafo_out" format="trafoxml"/> 179 <discover_datasets directory="out" pattern="__name_and_ext__"/>
180 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
181 </collection>
182 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
183 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
184 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
185 </collection>
186 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
187 <filter>OPTIONAL_OUTPUTS is None</filter>
188 </data>
189 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
190 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
191 </data>
207 </outputs> 192 </outputs>
208 <help>Corrects retention time distortions between maps based on common peptide identifications. 193 <tests>
209 194 <expand macro="autotest_MapAlignerIdentification"/>
210 195 <expand macro="manutest_MapAlignerIdentification"/>
211 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerIdentification.html</help> 196 </tests>
197 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
198
199
200 For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerIdentification.html]]></help>
201 <expand macro="references"/>
212 </tool> 202 </tool>