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comparison MapAlignerIdentification.xml @ 9:77b66c1c5415 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:29:16 +0000
parents 8434f070e939
children
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8:8434f070e939 9:77b66c1c5415
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description> 4 <description>Corrects retention time distortions between maps based on common peptide identifications</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MapAlignerIdentification</token> 6 <token name="@EXECUTABLE@">MapAlignerIdentification</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_cond.in && 16 mkdir in_cond.in &&
18 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else 20 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if 22 #end if
24 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir out && 24 mkdir out &&
26 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 25 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
27 #end if 26 #end if
29 mkdir trafo_out && 28 mkdir trafo_out &&
30 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 29 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
31 #end if 30 #end if
32 #if $design: 31 #if $design:
33 mkdir design && 32 mkdir design &&
34 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 33 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
35 #end if 34 #end if
36 #if $reference.file: 35 #if $reference.file:
37 mkdir reference.file && 36 mkdir reference.file &&
38 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && 37 cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
39 #end if 38 #end if
40 39
41 ## Main program call 40 ## Main program call
42 41
43 set -o pipefail && 42 set -o pipefail &&
86 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 85 <param name="in_select" type="select" label="Run tool in batch mode for -in">
87 <option value="no">No: process all datasets jointly</option> 86 <option value="no">No: process all datasets jointly</option>
88 <option value="yes">Yes: process each dataset in an independent job</option> 87 <option value="yes">Yes: process each dataset in an independent job</option>
89 </param> 88 </param>
90 <when value="no"> 89 <when value="no">
91 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/> 90 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="true" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
92 </when> 91 </when>
93 <when value="yes"> 92 <when value="yes">
94 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/> 93 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
95 </when> 94 </when>
96 </conditional> 95 </conditional>
97 <param argument="-design" type="data" format="tabular" optional="true" label="Input file containing the experimental design" help=" select tabular data sets(s)"/> 96 <param argument="-design" type="data" format="tabular" optional="true" label="Input file containing the experimental design" help=" select tabular data sets(s)"/>
98 <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output?" help=""/> 97 <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output?" help=""/>
99 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false"> 98 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
100 <param name="file" argument="-reference:file" type="data" format="consensusxml,featurexml,idxml,sqlite" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/> 99 <param name="file" argument="-reference:file" type="data" format="consensusxml,featurexml,idxml,sqlite" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
101 <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"/> 100 <param name="index" argument="-reference:index" type="integer" 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"/>
102 </section> 101 </section>
103 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 102 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
104 <param name="score_type" argument="-algorithm:score_type" type="text" optional="true" value="" label="Name of the score type to use for ranking and filtering (.oms input only)" help="If left empty, a score type is picked automatically"> 103 <param name="score_type" argument="-algorithm:score_type" type="text" optional="true" value="" label="Name of the score type to use for ranking and filtering (.oms input only)" help="If left empty, a score type is picked automatically">
105 <expand macro="list_string_san" name="score_type"/> 104 <expand macro="list_string_san" name="score_type"/>
106 </param> 105 </param>
107 <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only IDs above a score cut-off (parameter 'min_score') for alignment?" help=""/> 106 <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only IDs above a score cut-off (parameter 'min_score') for alignment?" help=""/>
108 <param name="min_score" argument="-algorithm:min_score" type="float" optional="true" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/> 107 <param name="min_score" argument="-algorithm:min_score" type="float" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
109 <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"/> 108 <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" 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"/>
110 <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"/> 109 <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" 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"/>
111 <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"/> 110 <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"/>
112 <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'"/> 111 <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'"/>
113 <param name="use_adducts" argument="-algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/> 112 <param name="use_adducts" argument="-algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/>
114 </section> 113 </section>
115 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> 114 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
116 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help=""> 115 <param name="type" argument="-model:type" type="select" label="Type of model" help="">
117 <option value="linear">linear</option> 116 <option value="linear">linear</option>
118 <option value="b_spline" selected="true">b_spline</option> 117 <option value="b_spline" selected="true">b_spline</option>
119 <option value="lowess">lowess</option> 118 <option value="lowess">lowess</option>
120 <option value="interpolated">interpolated</option> 119 <option value="interpolated">interpolated</option>
121 <expand macro="list_string_san" name="type"/> 120 <expand macro="list_string_san" name="type"/>
122 </param> 121 </param>
123 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false"> 122 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
124 <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'"/> 123 <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'"/>
125 <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help=""> 124 <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
126 <option value="1/x">1/x</option> 125 <option value="1/x">1/x</option>
127 <option value="1/x2">1/x2</option> 126 <option value="1/x2">1/x2</option>
128 <option value="ln(x)">ln(x)</option> 127 <option value="ln(x)">ln(x)</option>
129 <option value=""></option> 128 <option value="x" selected="true">x</option>
130 <expand macro="list_string_san" name="x_weight"/> 129 <expand macro="list_string_san" name="x_weight"/>
131 </param> 130 </param>
132 <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help=""> 131 <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
133 <option value="1/y">1/y</option> 132 <option value="1/y">1/y</option>
134 <option value="1/y2">1/y2</option> 133 <option value="1/y2">1/y2</option>
135 <option value="ln(y)">ln(y)</option> 134 <option value="ln(y)">ln(y)</option>
136 <option value=""></option> 135 <option value="y" selected="true">y</option>
137 <expand macro="list_string_san" name="y_weight"/> 136 <expand macro="list_string_san" name="y_weight"/>
138 </param> 137 </param>
139 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/> 138 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
140 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/> 139 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
141 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/> 140 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
142 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/> 141 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
143 </section> 142 </section>
144 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false"> 143 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
145 <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"/> 144 <param name="wavelength" argument="-model:b_spline:wavelength" type="float" 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"/>
146 <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"/> 145 <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" 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"/>
147 <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" 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)"> 146 <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" 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)">
148 <option value="linear" selected="true">linear</option> 147 <option value="linear" selected="true">linear</option>
149 <option value="b_spline">b_spline</option> 148 <option value="b_spline">b_spline</option>
150 <option value="constant">constant</option> 149 <option value="constant">constant</option>
151 <option value="global_linear">global_linear</option> 150 <option value="global_linear">global_linear</option>
152 <expand macro="list_string_san" name="extrapolate"/> 151 <expand macro="list_string_san" name="extrapolate"/>
153 </param> 152 </param>
154 <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=""/> 153 <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" 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=""/>
155 </section> 154 </section>
156 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false"> 155 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
157 <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"/> 156 <param name="span" argument="-model:lowess:span" type="float" 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"/>
158 <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=""/> 157 <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
159 <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"/> 158 <param name="delta" argument="-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="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"/>
160 <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" 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"> 159 <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" 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">
161 <option value="linear">linear</option> 160 <option value="linear">linear</option>
162 <option value="cspline" selected="true">cspline</option> 161 <option value="cspline" selected="true">cspline</option>
163 <option value="akima">akima</option> 162 <option value="akima">akima</option>
164 <expand macro="list_string_san" name="interpolation_type"/> 163 <expand macro="list_string_san" name="interpolation_type"/>
165 </param> 164 </param>
166 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" 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"> 165 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" 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">
167 <option value="two-point-linear">two-point-linear</option> 166 <option value="two-point-linear">two-point-linear</option>
168 <option value="four-point-linear" selected="true">four-point-linear</option> 167 <option value="four-point-linear" selected="true">four-point-linear</option>
169 <option value="global-linear">global-linear</option> 168 <option value="global-linear">global-linear</option>
170 <expand macro="list_string_san" name="extrapolation_type"/> 169 <expand macro="list_string_san" name="extrapolation_type"/>
171 </param> 170 </param>
172 </section> 171 </section>
173 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false"> 172 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
174 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help=""> 173 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
175 <option value="linear">linear</option> 174 <option value="linear">linear</option>
176 <option value="cspline" selected="true">cspline</option> 175 <option value="cspline" selected="true">cspline</option>
177 <option value="akima">akima</option> 176 <option value="akima">akima</option>
178 <expand macro="list_string_san" name="interpolation_type"/> 177 <expand macro="list_string_san" name="interpolation_type"/>
179 </param> 178 </param>
180 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" 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"> 179 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" 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">
181 <option value="two-point-linear" selected="true">two-point-linear</option> 180 <option value="two-point-linear" selected="true">two-point-linear</option>
182 <option value="four-point-linear">four-point-linear</option> 181 <option value="four-point-linear">four-point-linear</option>
183 <option value="global-linear">global-linear</option> 182 <option value="global-linear">global-linear</option>
184 <expand macro="list_string_san" name="extrapolation_type"/> 183 <expand macro="list_string_san" name="extrapolation_type"/>
185 </param> 184 </param>
186 </section> 185 </section>
187 </section> 186 </section>
188 <expand macro="adv_opts_macro"> 187 <expand macro="adv_opts_macro">
189 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 188 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
190 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 189 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
191 <expand macro="list_string_san" name="test"/> 190 <expand macro="list_string_san" name="test"/>
192 </param> 191 </param>
193 </expand> 192 </expand>
194 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 193 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
195 <option value="out_FLAG">out (Output files (same file type as 'in'))</option> 194 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
211 </data> 210 </data>
212 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 211 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
213 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 212 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
214 </data> 213 </data>
215 </outputs> 214 </outputs>
216 <tests><!-- TOPP_MapAlignerIdentification_1 --> 215 <tests>
216 <!-- TOPP_MapAlignerIdentification_1 -->
217 <test expect_num_outputs="2"> 217 <test expect_num_outputs="2">
218 <section name="adv_opts"> 218 <section name="adv_opts">
219 <param name="force" value="false"/> 219 <param name="force" value="false"/>
220 <param name="test" value="true"/> 220 <param name="test" value="true"/>
221 </section> 221 </section>
239 </section> 239 </section>
240 <section name="model"> 240 <section name="model">
241 <param name="type" value="b_spline"/> 241 <param name="type" value="b_spline"/>
242 <section name="linear"> 242 <section name="linear">
243 <param name="symmetric_regression" value="false"/> 243 <param name="symmetric_regression" value="false"/>
244 <param name="x_weight"/> 244 <param name="x_weight" value="x"/>
245 <param name="y_weight"/> 245 <param name="y_weight" value="y"/>
246 <param name="x_datum_min" value="1e-15"/> 246 <param name="x_datum_min" value="1e-15"/>
247 <param name="x_datum_max" value="1000000000000000.0"/> 247 <param name="x_datum_max" value="1000000000000000.0"/>
248 <param name="y_datum_min" value="1e-15"/> 248 <param name="y_datum_min" value="1e-15"/>
249 <param name="y_datum_max" value="1000000000000000.0"/> 249 <param name="y_datum_max" value="1000000000000000.0"/>
250 </section> 250 </section>
270 <output name="ctd_out" ftype="xml"> 270 <output name="ctd_out" ftype="xml">
271 <assert_contents> 271 <assert_contents>
272 <is_valid_xml/> 272 <is_valid_xml/>
273 </assert_contents> 273 </assert_contents>
274 </output> 274 </output>
275 <assert_stdout>
276 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
277 </assert_stdout>
275 </test> 278 </test>
276 <!-- TOPP_MapAlignerIdentification_2 --> 279 <!-- TOPP_MapAlignerIdentification_2 -->
277 <test expect_num_outputs="2"> 280 <test expect_num_outputs="2">
278 <section name="adv_opts"> 281 <section name="adv_opts">
279 <param name="force" value="false"/> 282 <param name="force" value="false"/>
300 </section> 303 </section>
301 <section name="model"> 304 <section name="model">
302 <param name="type" value="b_spline"/> 305 <param name="type" value="b_spline"/>
303 <section name="linear"> 306 <section name="linear">
304 <param name="symmetric_regression" value="false"/> 307 <param name="symmetric_regression" value="false"/>
305 <param name="x_weight"/> 308 <param name="x_weight" value="x"/>
306 <param name="y_weight"/> 309 <param name="y_weight" value="y"/>
307 <param name="x_datum_min" value="1e-15"/> 310 <param name="x_datum_min" value="1e-15"/>
308 <param name="x_datum_max" value="1000000000000000.0"/> 311 <param name="x_datum_max" value="1000000000000000.0"/>
309 <param name="y_datum_min" value="1e-15"/> 312 <param name="y_datum_min" value="1e-15"/>
310 <param name="y_datum_max" value="1000000000000000.0"/> 313 <param name="y_datum_max" value="1000000000000000.0"/>
311 </section> 314 </section>
331 <output name="ctd_out" ftype="xml"> 334 <output name="ctd_out" ftype="xml">
332 <assert_contents> 335 <assert_contents>
333 <is_valid_xml/> 336 <is_valid_xml/>
334 </assert_contents> 337 </assert_contents>
335 </output> 338 </output>
339 <assert_stdout>
340 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
341 </assert_stdout>
336 </test> 342 </test>
337 <!-- TOPP_MapAlignerIdentification_3 --> 343 <!-- TOPP_MapAlignerIdentification_3 -->
338 <test expect_num_outputs="2"> 344 <test expect_num_outputs="2">
339 <section name="adv_opts"> 345 <section name="adv_opts">
340 <param name="force" value="false"/> 346 <param name="force" value="false"/>
360 </section> 366 </section>
361 <section name="model"> 367 <section name="model">
362 <param name="type" value="b_spline"/> 368 <param name="type" value="b_spline"/>
363 <section name="linear"> 369 <section name="linear">
364 <param name="symmetric_regression" value="false"/> 370 <param name="symmetric_regression" value="false"/>
365 <param name="x_weight"/> 371 <param name="x_weight" value="x"/>
366 <param name="y_weight"/> 372 <param name="y_weight" value="y"/>
367 <param name="x_datum_min" value="1e-15"/> 373 <param name="x_datum_min" value="1e-15"/>
368 <param name="x_datum_max" value="1000000000000000.0"/> 374 <param name="x_datum_max" value="1000000000000000.0"/>
369 <param name="y_datum_min" value="1e-15"/> 375 <param name="y_datum_min" value="1e-15"/>
370 <param name="y_datum_max" value="1000000000000000.0"/> 376 <param name="y_datum_max" value="1000000000000000.0"/>
371 </section> 377 </section>
391 <output name="ctd_out" ftype="xml"> 397 <output name="ctd_out" ftype="xml">
392 <assert_contents> 398 <assert_contents>
393 <is_valid_xml/> 399 <is_valid_xml/>
394 </assert_contents> 400 </assert_contents>
395 </output> 401 </output>
402 <assert_stdout>
403 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
404 </assert_stdout>
396 </test> 405 </test>
397 <!-- TOPP_MapAlignerIdentification_4 --> 406 <!-- TOPP_MapAlignerIdentification_4 -->
398 <test expect_num_outputs="2"> 407 <test expect_num_outputs="2">
399 <section name="adv_opts"> 408 <section name="adv_opts">
400 <param name="force" value="false"/> 409 <param name="force" value="false"/>
420 </section> 429 </section>
421 <section name="model"> 430 <section name="model">
422 <param name="type" value="b_spline"/> 431 <param name="type" value="b_spline"/>
423 <section name="linear"> 432 <section name="linear">
424 <param name="symmetric_regression" value="false"/> 433 <param name="symmetric_regression" value="false"/>
425 <param name="x_weight"/> 434 <param name="x_weight" value="x"/>
426 <param name="y_weight"/> 435 <param name="y_weight" value="y"/>
427 <param name="x_datum_min" value="1e-15"/> 436 <param name="x_datum_min" value="1e-15"/>
428 <param name="x_datum_max" value="1000000000000000.0"/> 437 <param name="x_datum_max" value="1000000000000000.0"/>
429 <param name="y_datum_min" value="1e-15"/> 438 <param name="y_datum_min" value="1e-15"/>
430 <param name="y_datum_max" value="1000000000000000.0"/> 439 <param name="y_datum_max" value="1000000000000000.0"/>
431 </section> 440 </section>
451 <output name="ctd_out" ftype="xml"> 460 <output name="ctd_out" ftype="xml">
452 <assert_contents> 461 <assert_contents>
453 <is_valid_xml/> 462 <is_valid_xml/>
454 </assert_contents> 463 </assert_contents>
455 </output> 464 </output>
465 <assert_stdout>
466 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
467 </assert_stdout>
456 </test> 468 </test>
457 <!-- TOPP_MapAlignerIdentification_5 --> 469 <!-- TOPP_MapAlignerIdentification_5 -->
458 <test expect_num_outputs="2"> 470 <test expect_num_outputs="2">
459 <section name="adv_opts"> 471 <section name="adv_opts">
460 <param name="force" value="false"/> 472 <param name="force" value="false"/>
480 </section> 492 </section>
481 <section name="model"> 493 <section name="model">
482 <param name="type" value="b_spline"/> 494 <param name="type" value="b_spline"/>
483 <section name="linear"> 495 <section name="linear">
484 <param name="symmetric_regression" value="false"/> 496 <param name="symmetric_regression" value="false"/>
485 <param name="x_weight"/> 497 <param name="x_weight" value="x"/>
486 <param name="y_weight"/> 498 <param name="y_weight" value="y"/>
487 <param name="x_datum_min" value="1e-15"/> 499 <param name="x_datum_min" value="1e-15"/>
488 <param name="x_datum_max" value="1000000000000000.0"/> 500 <param name="x_datum_max" value="1000000000000000.0"/>
489 <param name="y_datum_min" value="1e-15"/> 501 <param name="y_datum_min" value="1e-15"/>
490 <param name="y_datum_max" value="1000000000000000.0"/> 502 <param name="y_datum_max" value="1000000000000000.0"/>
491 </section> 503 </section>
511 <output name="ctd_out" ftype="xml"> 523 <output name="ctd_out" ftype="xml">
512 <assert_contents> 524 <assert_contents>
513 <is_valid_xml/> 525 <is_valid_xml/>
514 </assert_contents> 526 </assert_contents>
515 </output> 527 </output>
528 <assert_stdout>
529 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
530 </assert_stdout>
516 </test> 531 </test>
517 <!-- TOPP_MapAlignerIdentification_6 --> 532 <!-- TOPP_MapAlignerIdentification_6 -->
518 <test expect_num_outputs="2"> 533 <test expect_num_outputs="2">
519 <section name="adv_opts"> 534 <section name="adv_opts">
520 <param name="force" value="false"/> 535 <param name="force" value="false"/>
541 </section> 556 </section>
542 <section name="model"> 557 <section name="model">
543 <param name="type" value="b_spline"/> 558 <param name="type" value="b_spline"/>
544 <section name="linear"> 559 <section name="linear">
545 <param name="symmetric_regression" value="false"/> 560 <param name="symmetric_regression" value="false"/>
546 <param name="x_weight"/> 561 <param name="x_weight" value="x"/>
547 <param name="y_weight"/> 562 <param name="y_weight" value="y"/>
548 <param name="x_datum_min" value="1e-15"/> 563 <param name="x_datum_min" value="1e-15"/>
549 <param name="x_datum_max" value="1000000000000000.0"/> 564 <param name="x_datum_max" value="1000000000000000.0"/>
550 <param name="y_datum_min" value="1e-15"/> 565 <param name="y_datum_min" value="1e-15"/>
551 <param name="y_datum_max" value="1000000000000000.0"/> 566 <param name="y_datum_max" value="1000000000000000.0"/>
552 </section> 567 </section>
572 <output name="ctd_out" ftype="xml"> 587 <output name="ctd_out" ftype="xml">
573 <assert_contents> 588 <assert_contents>
574 <is_valid_xml/> 589 <is_valid_xml/>
575 </assert_contents> 590 </assert_contents>
576 </output> 591 </output>
592 <assert_stdout>
593 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
594 </assert_stdout>
577 </test> 595 </test>
578 <!-- TOPP_MapAlignerIdentification_7 --> 596 <!-- TOPP_MapAlignerIdentification_7 -->
579 <test expect_num_outputs="3"> 597 <test expect_num_outputs="3">
580 <section name="adv_opts"> 598 <section name="adv_opts">
581 <param name="force" value="true"/> 599 <param name="force" value="true"/>
582 <param name="test" value="true"/> 600 <param name="test" value="true"/>
583 </section> 601 </section>
584 <conditional name="in_cond"> 602 <conditional name="in_cond">
585 <param name="in" value="MapAlignerIdentification_7_input1.idXML"/> 603 <param name="in" value="MapAlignerIdentification_7_input1_0.idXML"/>
586 </conditional> 604 </conditional>
587 <output_collection name="out" count="1"/> 605 <output_collection name="out" count="1"/>
588 <output_collection name="trafo_out" count="1"/> 606 <output_collection name="trafo_out" count="1"/>
589 <param name="store_original_rt" value="false"/> 607 <param name="store_original_rt" value="false"/>
590 <section name="reference"> 608 <section name="reference">
603 </section> 621 </section>
604 <section name="model"> 622 <section name="model">
605 <param name="type" value="b_spline"/> 623 <param name="type" value="b_spline"/>
606 <section name="linear"> 624 <section name="linear">
607 <param name="symmetric_regression" value="false"/> 625 <param name="symmetric_regression" value="false"/>
608 <param name="x_weight"/> 626 <param name="x_weight" value="x"/>
609 <param name="y_weight"/> 627 <param name="y_weight" value="y"/>
610 <param name="x_datum_min" value="1e-15"/> 628 <param name="x_datum_min" value="1e-15"/>
611 <param name="x_datum_max" value="1000000000000000.0"/> 629 <param name="x_datum_max" value="1000000000000000.0"/>
612 <param name="y_datum_min" value="1e-15"/> 630 <param name="y_datum_min" value="1e-15"/>
613 <param name="y_datum_max" value="1000000000000000.0"/> 631 <param name="y_datum_max" value="1000000000000000.0"/>
614 </section> 632 </section>
634 <output name="ctd_out" ftype="xml"> 652 <output name="ctd_out" ftype="xml">
635 <assert_contents> 653 <assert_contents>
636 <is_valid_xml/> 654 <is_valid_xml/>
637 </assert_contents> 655 </assert_contents>
638 </output> 656 </output>
657 <assert_stdout>
658 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
659 </assert_stdout>
639 </test> 660 </test>
640 <!-- TOPP_MapAlignerIdentification_8 --> 661 <!-- TOPP_MapAlignerIdentification_8 -->
641 <test expect_num_outputs="3"> 662 <test expect_num_outputs="3">
642 <section name="adv_opts"> 663 <section name="adv_opts">
643 <param name="force" value="false"/> 664 <param name="force" value="false"/>
665 </section> 686 </section>
666 <section name="model"> 687 <section name="model">
667 <param name="type" value="b_spline"/> 688 <param name="type" value="b_spline"/>
668 <section name="linear"> 689 <section name="linear">
669 <param name="symmetric_regression" value="false"/> 690 <param name="symmetric_regression" value="false"/>
670 <param name="x_weight"/> 691 <param name="x_weight" value="x"/>
671 <param name="y_weight"/> 692 <param name="y_weight" value="y"/>
672 <param name="x_datum_min" value="1e-15"/> 693 <param name="x_datum_min" value="1e-15"/>
673 <param name="x_datum_max" value="1000000000000000.0"/> 694 <param name="x_datum_max" value="1000000000000000.0"/>
674 <param name="y_datum_min" value="1e-15"/> 695 <param name="y_datum_min" value="1e-15"/>
675 <param name="y_datum_max" value="1000000000000000.0"/> 696 <param name="y_datum_max" value="1000000000000000.0"/>
676 </section> 697 </section>
696 <output name="ctd_out" ftype="xml"> 717 <output name="ctd_out" ftype="xml">
697 <assert_contents> 718 <assert_contents>
698 <is_valid_xml/> 719 <is_valid_xml/>
699 </assert_contents> 720 </assert_contents>
700 </output> 721 </output>
722 <assert_stdout>
723 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
724 </assert_stdout>
701 </test> 725 </test>
702 </tests> 726 </tests>
703 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications. 727 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
704 728
705 729
706 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerIdentification.html]]></help> 730 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerIdentification.html]]></help>
707 <expand macro="references"/> 731 <expand macro="references"/>
708 </tool> 732 </tool>