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comparison MapAlignerIdentification.xml @ 8:8434f070e939 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:22:07 +0000
parents 992bb7e5bf8d
children
comparison
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7:247aabec1b99 8:8434f070e939
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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 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>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 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])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 24 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out && 25 mkdir out &&
26 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
23 #end if 27 #end if
24 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 28 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir trafo_out && 29 mkdir trafo_out &&
30 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
26 #end if 31 #end if
27 #if $design: 32 #if $design:
28 mkdir design && 33 mkdir design &&
29 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 34 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
30 #end if 35 #end if
38 set -o pipefail && 43 set -o pipefail &&
39 @EXECUTABLE@ -write_ctd ./ && 44 @EXECUTABLE@ -write_ctd ./ &&
40 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 45 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
41 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 46 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
42 -in 47 -in
43 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 48 #if $in_cond.in_select == "no"
49 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
50 #else
51 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
52 #end if
44 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 53 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
45 -out 54 -out
46 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])} 55 ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), f.ext) for i, f in enumerate($in_cond.in) if f])}
47 #end if 56 #end if
48 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 57 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
49 -trafo_out 58 -trafo_out
50 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} 59 ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
51 #end if 60 #end if
52 #if $design: 61 #if $design:
53 -design 62 -design
54 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' 63 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
55 #end if 64 #end if
61 | tee '$stdout' 70 | tee '$stdout'
62 #end if 71 #end if
63 72
64 ## Postprocessing 73 ## Postprocessing
65 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 74 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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 _])} 75 ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
67 #end if 76 #end if
68 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 77 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
69 && mv '@EXECUTABLE@.ctd' '$ctd_out' 78 && mv '@EXECUTABLE@.ctd' '$ctd_out'
70 #end if]]></command> 79 #end if]]></command>
71 <configfiles> 80 <configfiles>
72 <inputs name="args_json" data_style="paths"/> 81 <inputs name="args_json" data_style="paths"/>
73 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 82 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
74 </configfiles> 83 </configfiles>
75 <inputs> 84 <inputs>
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)"/> 85 <conditional name="in_cond">
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)"/> 86 <param name="in_select" type="select" label="Run tool in batch mode for -in">
87 <option value="no">No: process all datasets jointly</option>
88 <option value="yes">Yes: process each dataset in an independent job</option>
89 </param>
90 <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)"/>
92 </when>
93 <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)"/>
95 </when>
96 </conditional>
97 <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=""/>
78 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false"> 99 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
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)"/> 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)"/>
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"/> 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"/>
81 </section> 102 </section>
82 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 103 <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"/> 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">
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"/> 105 <expand macro="list_string_san" name="score_type"/>
106 </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=""/>
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"/>
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"/> 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"/>
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"/> 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"/>
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"/> 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"/>
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'"/> 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'"/>
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=""/>
89 </section> 114 </section>
90 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> 115 <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=""> 116 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
92 <option value="linear">linear</option> 117 <option value="linear">linear</option>
93 <option value="b_spline" selected="true">b_spline</option> 118 <option value="b_spline" selected="true">b_spline</option>
94 <option value="lowess">lowess</option> 119 <option value="lowess">lowess</option>
95 <option value="interpolated">interpolated</option> 120 <option value="interpolated">interpolated</option>
96 <expand macro="list_string_san"/> 121 <expand macro="list_string_san" name="type"/>
97 </param> 122 </param>
98 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false"> 123 <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'"/> 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'"/>
100 <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help=""> 125 <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
101 <option value="">default (nothing chosen)</option>
102 <option value="1/x">1/x</option> 126 <option value="1/x">1/x</option>
103 <option value="1/x2">1/x2</option> 127 <option value="1/x2">1/x2</option>
104 <option value="ln(x)">ln(x)</option> 128 <option value="ln(x)">ln(x)</option>
105 <option value=""></option> 129 <option value=""></option>
106 <expand macro="list_string_san"/> 130 <expand macro="list_string_san" name="x_weight"/>
107 </param> 131 </param>
108 <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help=""> 132 <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
109 <option value="">default (nothing chosen)</option>
110 <option value="1/y">1/y</option> 133 <option value="1/y">1/y</option>
111 <option value="1/y2">1/y2</option> 134 <option value="1/y2">1/y2</option>
112 <option value="ln(y)">ln(y)</option> 135 <option value="ln(y)">ln(y)</option>
113 <option value=""></option> 136 <option value=""></option>
114 <expand macro="list_string_san"/> 137 <expand macro="list_string_san" name="y_weight"/>
115 </param> 138 </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=""/> 139 <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=""/> 140 <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=""/> 141 <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=""/> 142 <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> 143 </section>
121 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false"> 144 <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"/> 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"/>
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"/> 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"/>
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)"> 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)">
125 <option value="linear" selected="true">linear</option> 148 <option value="linear" selected="true">linear</option>
126 <option value="b_spline">b_spline</option> 149 <option value="b_spline">b_spline</option>
127 <option value="constant">constant</option> 150 <option value="constant">constant</option>
128 <option value="global_linear">global_linear</option> 151 <option value="global_linear">global_linear</option>
129 <expand macro="list_string_san"/> 152 <expand macro="list_string_san" name="extrapolate"/>
130 </param> 153 </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=""/> 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=""/>
132 </section> 155 </section>
133 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false"> 156 <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"/> 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"/>
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=""/> 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=""/>
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"/> 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"/>
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"> 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">
138 <option value="linear">linear</option> 161 <option value="linear">linear</option>
139 <option value="cspline" selected="true">cspline</option> 162 <option value="cspline" selected="true">cspline</option>
140 <option value="akima">akima</option> 163 <option value="akima">akima</option>
141 <expand macro="list_string_san"/> 164 <expand macro="list_string_san" name="interpolation_type"/>
142 </param> 165 </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"> 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">
144 <option value="two-point-linear">two-point-linear</option> 167 <option value="two-point-linear">two-point-linear</option>
145 <option value="four-point-linear" selected="true">four-point-linear</option> 168 <option value="four-point-linear" selected="true">four-point-linear</option>
146 <option value="global-linear">global-linear</option> 169 <option value="global-linear">global-linear</option>
147 <expand macro="list_string_san"/> 170 <expand macro="list_string_san" name="extrapolation_type"/>
148 </param> 171 </param>
149 </section> 172 </section>
150 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false"> 173 <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=""> 174 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
152 <option value="linear">linear</option> 175 <option value="linear">linear</option>
153 <option value="cspline" selected="true">cspline</option> 176 <option value="cspline" selected="true">cspline</option>
154 <option value="akima">akima</option> 177 <option value="akima">akima</option>
155 <expand macro="list_string_san"/> 178 <expand macro="list_string_san" name="interpolation_type"/>
156 </param> 179 </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"> 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">
158 <option value="two-point-linear" selected="true">two-point-linear</option> 181 <option value="two-point-linear" selected="true">two-point-linear</option>
159 <option value="four-point-linear">four-point-linear</option> 182 <option value="four-point-linear">four-point-linear</option>
160 <option value="global-linear">global-linear</option> 183 <option value="global-linear">global-linear</option>
161 <expand macro="list_string_san"/> 184 <expand macro="list_string_san" name="extrapolation_type"/>
162 </param> 185 </param>
163 </section> 186 </section>
164 </section> 187 </section>
165 <expand macro="adv_opts_macro"> 188 <expand macro="adv_opts_macro">
166 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 189 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> 190 <param 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"/> 191 <expand macro="list_string_san" name="test"/>
169 </param> 192 </param>
170 </expand> 193 </expand>
171 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 194 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
172 <option value="out_FLAG">out (Output files (same file type as 'in'))</option> 195 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
173 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option> 196 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
174 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 197 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
175 </param> 198 </param>
176 </inputs> 199 </inputs>
177 <outputs> 200 <outputs>
178 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> 201 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
179 <discover_datasets directory="out" pattern="__name_and_ext__"/> 202 <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
180 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> 203 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
181 </collection> 204 </collection>
182 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out"> 205 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
183 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/> 206 <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
184 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> 207 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
185 </collection> 208 </collection>
186 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> 209 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
187 <filter>OPTIONAL_OUTPUTS is None</filter> 210 <filter>OPTIONAL_OUTPUTS is None</filter>
188 </data> 211 </data>
189 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 212 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
190 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 213 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
191 </data> 214 </data>
192 </outputs> 215 </outputs>
193 <tests> 216 <tests><!-- TOPP_MapAlignerIdentification_1 -->
194 <expand macro="autotest_MapAlignerIdentification"/> 217 <test expect_num_outputs="2">
195 <expand macro="manutest_MapAlignerIdentification"/> 218 <section name="adv_opts">
219 <param name="force" value="false"/>
220 <param name="test" value="true"/>
221 </section>
222 <conditional name="in_cond">
223 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
224 </conditional>
225 <output_collection name="out" count="2"/>
226 <param name="store_original_rt" value="false"/>
227 <section name="reference">
228 <param name="index" value="0"/>
229 </section>
230 <section name="algorithm">
231 <param name="score_type" value=""/>
232 <param name="score_cutoff" value="false"/>
233 <param name="min_score" value="0.05"/>
234 <param name="min_run_occur" value="2"/>
235 <param name="max_rt_shift" value="0.0"/>
236 <param name="use_unassigned_peptides" value="true"/>
237 <param name="use_feature_rt" value="false"/>
238 <param name="use_adducts" value="true"/>
239 </section>
240 <section name="model">
241 <param name="type" value="b_spline"/>
242 <section name="linear">
243 <param name="symmetric_regression" value="false"/>
244 <param name="x_weight"/>
245 <param name="y_weight"/>
246 <param name="x_datum_min" value="1e-15"/>
247 <param name="x_datum_max" value="1000000000000000.0"/>
248 <param name="y_datum_min" value="1e-15"/>
249 <param name="y_datum_max" value="1000000000000000.0"/>
250 </section>
251 <section name="b_spline">
252 <param name="wavelength" value="0.0"/>
253 <param name="num_nodes" value="5"/>
254 <param name="extrapolate" value="linear"/>
255 <param name="boundary_condition" value="2"/>
256 </section>
257 <section name="lowess">
258 <param name="span" value="0.666666666666667"/>
259 <param name="num_iterations" value="3"/>
260 <param name="delta" value="-1.0"/>
261 <param name="interpolation_type" value="cspline"/>
262 <param name="extrapolation_type" value="four-point-linear"/>
263 </section>
264 <section name="interpolated">
265 <param name="interpolation_type" value="cspline"/>
266 <param name="extrapolation_type" value="two-point-linear"/>
267 </section>
268 </section>
269 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
270 <output name="ctd_out" ftype="xml">
271 <assert_contents>
272 <is_valid_xml/>
273 </assert_contents>
274 </output>
275 </test>
276 <!-- TOPP_MapAlignerIdentification_2 -->
277 <test expect_num_outputs="2">
278 <section name="adv_opts">
279 <param name="force" value="false"/>
280 <param name="test" value="true"/>
281 </section>
282 <conditional name="in_cond">
283 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
284 </conditional>
285 <output_collection name="out" count="1"/>
286 <param name="store_original_rt" value="false"/>
287 <section name="reference">
288 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
289 <param name="index" value="0"/>
290 </section>
291 <section name="algorithm">
292 <param name="score_type" value=""/>
293 <param name="score_cutoff" value="false"/>
294 <param name="min_score" value="0.05"/>
295 <param name="min_run_occur" value="2"/>
296 <param name="max_rt_shift" value="0.0"/>
297 <param name="use_unassigned_peptides" value="true"/>
298 <param name="use_feature_rt" value="false"/>
299 <param name="use_adducts" value="true"/>
300 </section>
301 <section name="model">
302 <param name="type" value="b_spline"/>
303 <section name="linear">
304 <param name="symmetric_regression" value="false"/>
305 <param name="x_weight"/>
306 <param name="y_weight"/>
307 <param name="x_datum_min" value="1e-15"/>
308 <param name="x_datum_max" value="1000000000000000.0"/>
309 <param name="y_datum_min" value="1e-15"/>
310 <param name="y_datum_max" value="1000000000000000.0"/>
311 </section>
312 <section name="b_spline">
313 <param name="wavelength" value="0.0"/>
314 <param name="num_nodes" value="5"/>
315 <param name="extrapolate" value="linear"/>
316 <param name="boundary_condition" value="2"/>
317 </section>
318 <section name="lowess">
319 <param name="span" value="0.666666666666667"/>
320 <param name="num_iterations" value="3"/>
321 <param name="delta" value="-1.0"/>
322 <param name="interpolation_type" value="cspline"/>
323 <param name="extrapolation_type" value="four-point-linear"/>
324 </section>
325 <section name="interpolated">
326 <param name="interpolation_type" value="cspline"/>
327 <param name="extrapolation_type" value="two-point-linear"/>
328 </section>
329 </section>
330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
331 <output name="ctd_out" ftype="xml">
332 <assert_contents>
333 <is_valid_xml/>
334 </assert_contents>
335 </output>
336 </test>
337 <!-- TOPP_MapAlignerIdentification_3 -->
338 <test expect_num_outputs="2">
339 <section name="adv_opts">
340 <param name="force" value="false"/>
341 <param name="test" value="true"/>
342 </section>
343 <conditional name="in_cond">
344 <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
345 </conditional>
346 <output_collection name="out" count="2"/>
347 <param name="store_original_rt" value="false"/>
348 <section name="reference">
349 <param name="index" value="1"/>
350 </section>
351 <section name="algorithm">
352 <param name="score_type" value=""/>
353 <param name="score_cutoff" value="false"/>
354 <param name="min_score" value="0.05"/>
355 <param name="min_run_occur" value="2"/>
356 <param name="max_rt_shift" value="0.0"/>
357 <param name="use_unassigned_peptides" value="true"/>
358 <param name="use_feature_rt" value="false"/>
359 <param name="use_adducts" value="true"/>
360 </section>
361 <section name="model">
362 <param name="type" value="b_spline"/>
363 <section name="linear">
364 <param name="symmetric_regression" value="false"/>
365 <param name="x_weight"/>
366 <param name="y_weight"/>
367 <param name="x_datum_min" value="1e-15"/>
368 <param name="x_datum_max" value="1000000000000000.0"/>
369 <param name="y_datum_min" value="1e-15"/>
370 <param name="y_datum_max" value="1000000000000000.0"/>
371 </section>
372 <section name="b_spline">
373 <param name="wavelength" value="0.0"/>
374 <param name="num_nodes" value="5"/>
375 <param name="extrapolate" value="linear"/>
376 <param name="boundary_condition" value="2"/>
377 </section>
378 <section name="lowess">
379 <param name="span" value="0.666666666666667"/>
380 <param name="num_iterations" value="3"/>
381 <param name="delta" value="-1.0"/>
382 <param name="interpolation_type" value="cspline"/>
383 <param name="extrapolation_type" value="four-point-linear"/>
384 </section>
385 <section name="interpolated">
386 <param name="interpolation_type" value="cspline"/>
387 <param name="extrapolation_type" value="two-point-linear"/>
388 </section>
389 </section>
390 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
391 <output name="ctd_out" ftype="xml">
392 <assert_contents>
393 <is_valid_xml/>
394 </assert_contents>
395 </output>
396 </test>
397 <!-- TOPP_MapAlignerIdentification_4 -->
398 <test expect_num_outputs="2">
399 <section name="adv_opts">
400 <param name="force" value="false"/>
401 <param name="test" value="true"/>
402 </section>
403 <conditional name="in_cond">
404 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
405 </conditional>
406 <output_collection name="out" count="2"/>
407 <param name="store_original_rt" value="false"/>
408 <section name="reference">
409 <param name="index" value="2"/>
410 </section>
411 <section name="algorithm">
412 <param name="score_type" value=""/>
413 <param name="score_cutoff" value="false"/>
414 <param name="min_score" value="0.05"/>
415 <param name="min_run_occur" value="2"/>
416 <param name="max_rt_shift" value="0.0"/>
417 <param name="use_unassigned_peptides" value="true"/>
418 <param name="use_feature_rt" value="false"/>
419 <param name="use_adducts" value="true"/>
420 </section>
421 <section name="model">
422 <param name="type" value="b_spline"/>
423 <section name="linear">
424 <param name="symmetric_regression" value="false"/>
425 <param name="x_weight"/>
426 <param name="y_weight"/>
427 <param name="x_datum_min" value="1e-15"/>
428 <param name="x_datum_max" value="1000000000000000.0"/>
429 <param name="y_datum_min" value="1e-15"/>
430 <param name="y_datum_max" value="1000000000000000.0"/>
431 </section>
432 <section name="b_spline">
433 <param name="wavelength" value="0.0"/>
434 <param name="num_nodes" value="5"/>
435 <param name="extrapolate" value="linear"/>
436 <param name="boundary_condition" value="2"/>
437 </section>
438 <section name="lowess">
439 <param name="span" value="0.666666666666667"/>
440 <param name="num_iterations" value="3"/>
441 <param name="delta" value="-1.0"/>
442 <param name="interpolation_type" value="cspline"/>
443 <param name="extrapolation_type" value="four-point-linear"/>
444 </section>
445 <section name="interpolated">
446 <param name="interpolation_type" value="cspline"/>
447 <param name="extrapolation_type" value="two-point-linear"/>
448 </section>
449 </section>
450 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
451 <output name="ctd_out" ftype="xml">
452 <assert_contents>
453 <is_valid_xml/>
454 </assert_contents>
455 </output>
456 </test>
457 <!-- TOPP_MapAlignerIdentification_5 -->
458 <test expect_num_outputs="2">
459 <section name="adv_opts">
460 <param name="force" value="false"/>
461 <param name="test" value="true"/>
462 </section>
463 <conditional name="in_cond">
464 <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
465 </conditional>
466 <output_collection name="out" count="2"/>
467 <param name="store_original_rt" value="false"/>
468 <section name="reference">
469 <param name="index" value="0"/>
470 </section>
471 <section name="algorithm">
472 <param name="score_type" value=""/>
473 <param name="score_cutoff" value="false"/>
474 <param name="min_score" value="0.05"/>
475 <param name="min_run_occur" value="2"/>
476 <param name="max_rt_shift" value="0.0"/>
477 <param name="use_unassigned_peptides" value="true"/>
478 <param name="use_feature_rt" value="false"/>
479 <param name="use_adducts" value="true"/>
480 </section>
481 <section name="model">
482 <param name="type" value="b_spline"/>
483 <section name="linear">
484 <param name="symmetric_regression" value="false"/>
485 <param name="x_weight"/>
486 <param name="y_weight"/>
487 <param name="x_datum_min" value="1e-15"/>
488 <param name="x_datum_max" value="1000000000000000.0"/>
489 <param name="y_datum_min" value="1e-15"/>
490 <param name="y_datum_max" value="1000000000000000.0"/>
491 </section>
492 <section name="b_spline">
493 <param name="wavelength" value="0.0"/>
494 <param name="num_nodes" value="5"/>
495 <param name="extrapolate" value="linear"/>
496 <param name="boundary_condition" value="2"/>
497 </section>
498 <section name="lowess">
499 <param name="span" value="0.666666666666667"/>
500 <param name="num_iterations" value="3"/>
501 <param name="delta" value="-1.0"/>
502 <param name="interpolation_type" value="cspline"/>
503 <param name="extrapolation_type" value="four-point-linear"/>
504 </section>
505 <section name="interpolated">
506 <param name="interpolation_type" value="cspline"/>
507 <param name="extrapolation_type" value="two-point-linear"/>
508 </section>
509 </section>
510 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
511 <output name="ctd_out" ftype="xml">
512 <assert_contents>
513 <is_valid_xml/>
514 </assert_contents>
515 </output>
516 </test>
517 <!-- TOPP_MapAlignerIdentification_6 -->
518 <test expect_num_outputs="2">
519 <section name="adv_opts">
520 <param name="force" value="false"/>
521 <param name="test" value="true"/>
522 </section>
523 <conditional name="in_cond">
524 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
525 </conditional>
526 <output_collection name="trafo_out" count="1"/>
527 <param name="store_original_rt" value="false"/>
528 <section name="reference">
529 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
530 <param name="index" value="0"/>
531 </section>
532 <section name="algorithm">
533 <param name="score_type" value=""/>
534 <param name="score_cutoff" value="false"/>
535 <param name="min_score" value="0.05"/>
536 <param name="min_run_occur" value="2"/>
537 <param name="max_rt_shift" value="0.0"/>
538 <param name="use_unassigned_peptides" value="true"/>
539 <param name="use_feature_rt" value="false"/>
540 <param name="use_adducts" value="true"/>
541 </section>
542 <section name="model">
543 <param name="type" value="b_spline"/>
544 <section name="linear">
545 <param name="symmetric_regression" value="false"/>
546 <param name="x_weight"/>
547 <param name="y_weight"/>
548 <param name="x_datum_min" value="1e-15"/>
549 <param name="x_datum_max" value="1000000000000000.0"/>
550 <param name="y_datum_min" value="1e-15"/>
551 <param name="y_datum_max" value="1000000000000000.0"/>
552 </section>
553 <section name="b_spline">
554 <param name="wavelength" value="0.0"/>
555 <param name="num_nodes" value="5"/>
556 <param name="extrapolate" value="linear"/>
557 <param name="boundary_condition" value="2"/>
558 </section>
559 <section name="lowess">
560 <param name="span" value="0.666666666666667"/>
561 <param name="num_iterations" value="3"/>
562 <param name="delta" value="-1.0"/>
563 <param name="interpolation_type" value="cspline"/>
564 <param name="extrapolation_type" value="four-point-linear"/>
565 </section>
566 <section name="interpolated">
567 <param name="interpolation_type" value="cspline"/>
568 <param name="extrapolation_type" value="two-point-linear"/>
569 </section>
570 </section>
571 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
572 <output name="ctd_out" ftype="xml">
573 <assert_contents>
574 <is_valid_xml/>
575 </assert_contents>
576 </output>
577 </test>
578 <!-- TOPP_MapAlignerIdentification_7 -->
579 <test expect_num_outputs="3">
580 <section name="adv_opts">
581 <param name="force" value="true"/>
582 <param name="test" value="true"/>
583 </section>
584 <conditional name="in_cond">
585 <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
586 </conditional>
587 <output_collection name="out" count="1"/>
588 <output_collection name="trafo_out" count="1"/>
589 <param name="store_original_rt" value="false"/>
590 <section name="reference">
591 <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
592 <param name="index" value="0"/>
593 </section>
594 <section name="algorithm">
595 <param name="score_type" value=""/>
596 <param name="score_cutoff" value="false"/>
597 <param name="min_score" value="0.05"/>
598 <param name="min_run_occur" value="2"/>
599 <param name="max_rt_shift" value="0.5"/>
600 <param name="use_unassigned_peptides" value="true"/>
601 <param name="use_feature_rt" value="false"/>
602 <param name="use_adducts" value="true"/>
603 </section>
604 <section name="model">
605 <param name="type" value="b_spline"/>
606 <section name="linear">
607 <param name="symmetric_regression" value="false"/>
608 <param name="x_weight"/>
609 <param name="y_weight"/>
610 <param name="x_datum_min" value="1e-15"/>
611 <param name="x_datum_max" value="1000000000000000.0"/>
612 <param name="y_datum_min" value="1e-15"/>
613 <param name="y_datum_max" value="1000000000000000.0"/>
614 </section>
615 <section name="b_spline">
616 <param name="wavelength" value="0.0"/>
617 <param name="num_nodes" value="5"/>
618 <param name="extrapolate" value="linear"/>
619 <param name="boundary_condition" value="2"/>
620 </section>
621 <section name="lowess">
622 <param name="span" value="0.666666666666667"/>
623 <param name="num_iterations" value="3"/>
624 <param name="delta" value="-1.0"/>
625 <param name="interpolation_type" value="cspline"/>
626 <param name="extrapolation_type" value="four-point-linear"/>
627 </section>
628 <section name="interpolated">
629 <param name="interpolation_type" value="cspline"/>
630 <param name="extrapolation_type" value="two-point-linear"/>
631 </section>
632 </section>
633 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
634 <output name="ctd_out" ftype="xml">
635 <assert_contents>
636 <is_valid_xml/>
637 </assert_contents>
638 </output>
639 </test>
640 <!-- TOPP_MapAlignerIdentification_8 -->
641 <test expect_num_outputs="3">
642 <section name="adv_opts">
643 <param name="force" value="false"/>
644 <param name="test" value="true"/>
645 </section>
646 <conditional name="in_cond">
647 <param name="in" value="MapAlignerIdentification_8_input1.oms"/>
648 </conditional>
649 <output_collection name="out" count="1"/>
650 <output_collection name="trafo_out" count="1"/>
651 <param name="store_original_rt" value="true"/>
652 <section name="reference">
653 <param name="file" value="MapAlignerIdentification_8_input2.oms"/>
654 <param name="index" value="0"/>
655 </section>
656 <section name="algorithm">
657 <param name="score_type" value=""/>
658 <param name="score_cutoff" value="false"/>
659 <param name="min_score" value="0.05"/>
660 <param name="min_run_occur" value="2"/>
661 <param name="max_rt_shift" value="0.5"/>
662 <param name="use_unassigned_peptides" value="true"/>
663 <param name="use_feature_rt" value="false"/>
664 <param name="use_adducts" value="true"/>
665 </section>
666 <section name="model">
667 <param name="type" value="b_spline"/>
668 <section name="linear">
669 <param name="symmetric_regression" value="false"/>
670 <param name="x_weight"/>
671 <param name="y_weight"/>
672 <param name="x_datum_min" value="1e-15"/>
673 <param name="x_datum_max" value="1000000000000000.0"/>
674 <param name="y_datum_min" value="1e-15"/>
675 <param name="y_datum_max" value="1000000000000000.0"/>
676 </section>
677 <section name="b_spline">
678 <param name="wavelength" value="0.0"/>
679 <param name="num_nodes" value="5"/>
680 <param name="extrapolate" value="linear"/>
681 <param name="boundary_condition" value="2"/>
682 </section>
683 <section name="lowess">
684 <param name="span" value="0.666666666666667"/>
685 <param name="num_iterations" value="3"/>
686 <param name="delta" value="-1.0"/>
687 <param name="interpolation_type" value="cspline"/>
688 <param name="extrapolation_type" value="four-point-linear"/>
689 </section>
690 <section name="interpolated">
691 <param name="interpolation_type" value="cspline"/>
692 <param name="extrapolation_type" value="two-point-linear"/>
693 </section>
694 </section>
695 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
696 <output name="ctd_out" ftype="xml">
697 <assert_contents>
698 <is_valid_xml/>
699 </assert_contents>
700 </output>
701 </test>
196 </tests> 702 </tests>
197 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications. 703 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
198 704
199 705
200 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerIdentification.html]]></help> 706 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerIdentification.html]]></help>
201 <expand macro="references"/> 707 <expand macro="references"/>
202 </tool> 708 </tool>