Mercurial > repos > galaxyp > openms_mapaligneridentification
comparison MapAlignerIdentification.xml @ 4:bf50f9eb1dcb draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 19:44:14 +0000 |
parents | 1f0a9c3cb526 |
children | 992bb7e5bf8d |
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3:ce546b0bf9c2 | 4:bf50f9eb1dcb |
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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="""/> | 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 > 1, the final value in seconds; if <= 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) <br>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. <br>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. <br>If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 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. <br>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> |