Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd

comparison FeatureLinkerUnlabeledKD.xml @ 12:718c0e2904cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:58:38 +0000
parents 7a9d97cfe93c
children 902d0f778dcf
comparison
equal deleted inserted replaced
11:5690b9865216 12:718c0e2904cb
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="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Groups corresponding features from multiple maps.</description> 5 <description>Groups corresponding features from multiple maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</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 mkdir out && 24 mkdir out &&
22 #if $design: 25 #if $design:
23 mkdir design && 26 mkdir design &&
24 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
25 #end if 28 #end if
29 set -o pipefail && 32 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ && 33 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in 36 -in
34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 37 #if $in_cond.in_select == "no"
38 ${' '.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])}
39 #else
40 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
41 #end if
35 -out 42 -out
36 'out/output.${gxy2omsext("consensusxml")}' 43 'out/output.${gxy2omsext("consensusxml")}'
37 #if $design: 44 #if $design:
38 -design 45 -design
39 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' 46 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
47 <configfiles> 54 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 57 </configfiles>
51 <inputs> 58 <inputs>
52 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> 59 <conditional name="in_cond">
53 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> 60 <param name="in_select" type="select" label="Run tool in batch mode for -in">
54 <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/> 61 <option value="no">No: process all datasets jointly</option>
62 <option value="yes">Yes: process each dataset in an independent job</option>
63 </param>
64 <when value="no">
65 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
66 </when>
67 <when value="yes">
68 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
69 </when>
70 </conditional>
71 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
72 <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
56 <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of m/z tolerance" help=""> 74 <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" label="Unit of m/z tolerance" help="">
57 <option value="ppm" selected="true">ppm</option> 75 <option value="ppm" selected="true">ppm</option>
58 <option value="Da">Da</option> 76 <option value="Da">Da</option>
59 <expand macro="list_string_san"/> 77 <expand macro="list_string_san" name="mz_unit"/>
60 </param> 78 </param>
61 <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="Number of partitions in m/z space" help=""/> 79 <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="Number of partitions in m/z space" help=""/>
62 <section name="warp" title="" help="" expanded="false"> 80 <section name="warp" title="" help="" expanded="false">
63 <param name="enabled" argument="-algorithm:warp:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help=""/> 81 <param name="enabled" argument="-algorithm:warp:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help=""/>
64 <param name="rt_tol" argument="-algorithm:warp:rt_tol" type="float" optional="true" min="0.0" value="100.0" label="Width of RT tolerance window (sec)" help=""/> 82 <param name="rt_tol" argument="-algorithm:warp:rt_tol" type="float" optional="true" min="0.0" value="100.0" label="Width of RT tolerance window (sec)" help=""/>
68 <param name="max_nr_conflicts" argument="-algorithm:warp:max_nr_conflicts" type="integer" optional="true" min="-1" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help=""/> 86 <param name="max_nr_conflicts" argument="-algorithm:warp:max_nr_conflicts" type="integer" optional="true" min="-1" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help=""/>
69 </section> 87 </section>
70 <section name="link" title="" help="" expanded="false"> 88 <section name="link" title="" help="" expanded="false">
71 <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" optional="true" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/> 89 <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" optional="true" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/>
72 <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" optional="true" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/> 90 <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" optional="true" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/>
73 <param name="charge_merging" argument="-algorithm:link:charge_merging" display="radio" type="select" optional="false" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)"> 91 <param name="charge_merging" argument="-algorithm:link:charge_merging" type="select" optional="true" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)">
74 <option value="Identical">Identical</option> 92 <option value="Identical">Identical</option>
75 <option value="With_charge_zero" selected="true">With_charge_zero</option> 93 <option value="With_charge_zero" selected="true">With_charge_zero</option>
76 <option value="Any">Any</option> 94 <option value="Any">Any</option>
77 <expand macro="list_string_san"/> 95 <expand macro="list_string_san" name="charge_merging"/>
78 </param> 96 </param>
79 <param name="adduct_merging" argument="-algorithm:link:adduct_merging" display="radio" type="select" optional="false" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help=""> 97 <param name="adduct_merging" argument="-algorithm:link:adduct_merging" type="select" optional="true" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help="">
80 <option value="Identical">Identical</option> 98 <option value="Identical">Identical</option>
81 <option value="With_unknown_adducts">With_unknown_adducts</option> 99 <option value="With_unknown_adducts">With_unknown_adducts</option>
82 <option value="Any" selected="true">Any</option> 100 <option value="Any" selected="true">Any</option>
83 <expand macro="list_string_san"/> 101 <expand macro="list_string_san" name="adduct_merging"/>
84 </param> 102 </param>
85 </section> 103 </section>
86 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> 104 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
87 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 105 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
88 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/> 106 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
92 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/> 110 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
93 </section> 111 </section>
94 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false"> 112 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
95 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 113 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
96 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/> 114 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/>
97 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> 115 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
98 <option value="enabled" selected="true">enabled</option> 116 <option value="enabled" selected="true">enabled</option>
99 <option value="disabled">disabled</option> 117 <option value="disabled">disabled</option>
100 <expand macro="list_string_san"/> 118 <expand macro="list_string_san" name="log_transform"/>
101 </param> 119 </param>
102 </section> 120 </section>
103 <section name="LOWESS" title="LOWESS parameters for internal RT transformations (only relevant if 'warp:enabled' is set to 'true')" help="" expanded="false"> 121 <section name="LOWESS" title="LOWESS parameters for internal RT transformations (only relevant if 'warp:enabled' is set to 'true')" help="" expanded="false">
104 <param name="span" argument="-algorithm: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"/> 122 <param name="span" argument="-algorithm: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"/>
105 <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/> 123 <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
106 <param name="delta" argument="-algorithm: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"/> 124 <param name="delta" argument="-algorithm: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"/>
107 <param name="interpolation_type" argument="-algorithm: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"> 125 <param name="interpolation_type" argument="-algorithm: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">
108 <option value="linear">linear</option> 126 <option value="linear">linear</option>
109 <option value="cspline" selected="true">cspline</option> 127 <option value="cspline" selected="true">cspline</option>
110 <option value="akima">akima</option> 128 <option value="akima">akima</option>
111 <expand macro="list_string_san"/> 129 <expand macro="list_string_san" name="interpolation_type"/>
112 </param> 130 </param>
113 <param name="extrapolation_type" argument="-algorithm: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"> 131 <param name="extrapolation_type" argument="-algorithm: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">
114 <option value="two-point-linear">two-point-linear</option> 132 <option value="two-point-linear">two-point-linear</option>
115 <option value="four-point-linear" selected="true">four-point-linear</option> 133 <option value="four-point-linear" selected="true">four-point-linear</option>
116 <option value="global-linear">global-linear</option> 134 <option value="global-linear">global-linear</option>
117 <expand macro="list_string_san"/> 135 <expand macro="list_string_san" name="extrapolation_type"/>
118 </param> 136 </param>
119 </section> 137 </section>
120 </section> 138 </section>
121 <expand macro="adv_opts_macro"> 139 <expand macro="adv_opts_macro">
122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 140 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
123 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 141 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
124 <expand macro="list_string_san"/> 142 <expand macro="list_string_san" name="test"/>
125 </param> 143 </param>
126 </expand> 144 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 145 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 146 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
129 </param> 147 </param>
132 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 150 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 151 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 152 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
135 </data> 153 </data>
136 </outputs> 154 </outputs>
137 <tests> 155 <tests><!-- TOPP_FeatureLinkerUnlabeledKD_1 -->
138 <expand macro="autotest_FeatureLinkerUnlabeledKD"/> 156 <test expect_num_outputs="2">
139 <expand macro="manutest_FeatureLinkerUnlabeledKD"/> 157 <section name="adv_opts">
158 <param name="force" value="false"/>
159 <param name="test" value="true"/>
160 </section>
161 <conditional name="in_cond">
162 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
163 </conditional>
164 <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
165 <param name="keep_subelements" value="false"/>
166 <section name="algorithm">
167 <param name="mz_unit" value="Da"/>
168 <param name="nr_partitions" value="1"/>
169 <section name="warp">
170 <param name="enabled" value="false"/>
171 <param name="rt_tol" value="100.0"/>
172 <param name="mz_tol" value="0.3"/>
173 <param name="max_pairwise_log_fc" value="0.5"/>
174 <param name="min_rel_cc_size" value="0.5"/>
175 <param name="max_nr_conflicts" value="0"/>
176 </section>
177 <section name="link">
178 <param name="rt_tol" value="100.0"/>
179 <param name="mz_tol" value="0.3"/>
180 <param name="charge_merging" value="With_charge_zero"/>
181 <param name="adduct_merging" value="Any"/>
182 </section>
183 <section name="distance_RT">
184 <param name="exponent" value="1.0"/>
185 <param name="weight" value="1.0"/>
186 </section>
187 <section name="distance_MZ">
188 <param name="exponent" value="2.0"/>
189 <param name="weight" value="1.0"/>
190 </section>
191 <section name="distance_intensity">
192 <param name="exponent" value="1.0"/>
193 <param name="weight" value="1.0"/>
194 <param name="log_transform" value="enabled"/>
195 </section>
196 <section name="LOWESS">
197 <param name="span" value="0.666666666666667"/>
198 <param name="num_iterations" value="3"/>
199 <param name="delta" value="-1.0"/>
200 <param name="interpolation_type" value="cspline"/>
201 <param name="extrapolation_type" value="four-point-linear"/>
202 </section>
203 </section>
204 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
205 <output name="ctd_out" ftype="xml">
206 <assert_contents>
207 <is_valid_xml/>
208 </assert_contents>
209 </output>
210 </test>
211 <!-- TOPP_FeatureLinkerUnlabeledKD_2 -->
212 <test expect_num_outputs="2">
213 <section name="adv_opts">
214 <param name="force" value="false"/>
215 <param name="test" value="true"/>
216 </section>
217 <conditional name="in_cond">
218 <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
219 </conditional>
220 <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
221 <param name="keep_subelements" value="true"/>
222 <section name="algorithm">
223 <param name="mz_unit" value="Da"/>
224 <param name="nr_partitions" value="99999"/>
225 <section name="warp">
226 <param name="enabled" value="false"/>
227 <param name="rt_tol" value="100.0"/>
228 <param name="mz_tol" value="0.3"/>
229 <param name="max_pairwise_log_fc" value="0.5"/>
230 <param name="min_rel_cc_size" value="0.5"/>
231 <param name="max_nr_conflicts" value="0"/>
232 </section>
233 <section name="link">
234 <param name="rt_tol" value="100.0"/>
235 <param name="mz_tol" value="0.3"/>
236 <param name="charge_merging" value="With_charge_zero"/>
237 <param name="adduct_merging" value="Any"/>
238 </section>
239 <section name="distance_RT">
240 <param name="exponent" value="1.0"/>
241 <param name="weight" value="1.0"/>
242 </section>
243 <section name="distance_MZ">
244 <param name="exponent" value="2.0"/>
245 <param name="weight" value="1.0"/>
246 </section>
247 <section name="distance_intensity">
248 <param name="exponent" value="1.0"/>
249 <param name="weight" value="1.0"/>
250 <param name="log_transform" value="enabled"/>
251 </section>
252 <section name="LOWESS">
253 <param name="span" value="0.666666666666667"/>
254 <param name="num_iterations" value="3"/>
255 <param name="delta" value="-1.0"/>
256 <param name="interpolation_type" value="cspline"/>
257 <param name="extrapolation_type" value="four-point-linear"/>
258 </section>
259 </section>
260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
261 <output name="ctd_out" ftype="xml">
262 <assert_contents>
263 <is_valid_xml/>
264 </assert_contents>
265 </output>
266 </test>
267 <!-- TOPP_FeatureLinkerUnlabeledKD_3 -->
268 <test expect_num_outputs="2">
269 <section name="adv_opts">
270 <param name="force" value="false"/>
271 <param name="test" value="true"/>
272 </section>
273 <conditional name="in_cond">
274 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
275 </conditional>
276 <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
277 <param name="keep_subelements" value="false"/>
278 <section name="algorithm">
279 <param name="mz_unit" value="Da"/>
280 <param name="nr_partitions" value="100"/>
281 <section name="warp">
282 <param name="enabled" value="false"/>
283 <param name="rt_tol" value="100.0"/>
284 <param name="mz_tol" value="0.3"/>
285 <param name="max_pairwise_log_fc" value="0.5"/>
286 <param name="min_rel_cc_size" value="0.5"/>
287 <param name="max_nr_conflicts" value="0"/>
288 </section>
289 <section name="link">
290 <param name="rt_tol" value="100.0"/>
291 <param name="mz_tol" value="0.3"/>
292 <param name="charge_merging" value="With_charge_zero"/>
293 <param name="adduct_merging" value="Any"/>
294 </section>
295 <section name="distance_RT">
296 <param name="exponent" value="1.0"/>
297 <param name="weight" value="1.0"/>
298 </section>
299 <section name="distance_MZ">
300 <param name="exponent" value="2.0"/>
301 <param name="weight" value="1.0"/>
302 </section>
303 <section name="distance_intensity">
304 <param name="exponent" value="1.0"/>
305 <param name="weight" value="1.0"/>
306 <param name="log_transform" value="enabled"/>
307 </section>
308 <section name="LOWESS">
309 <param name="span" value="0.666666666666667"/>
310 <param name="num_iterations" value="3"/>
311 <param name="delta" value="-1.0"/>
312 <param name="interpolation_type" value="cspline"/>
313 <param name="extrapolation_type" value="four-point-linear"/>
314 </section>
315 </section>
316 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
317 <output name="ctd_out" ftype="xml">
318 <assert_contents>
319 <is_valid_xml/>
320 </assert_contents>
321 </output>
322 </test>
323 <!-- TOPP_FeatureLinkerUnlabeledKD_4 -->
324 <test expect_num_outputs="2">
325 <section name="adv_opts">
326 <param name="force" value="false"/>
327 <param name="test" value="true"/>
328 </section>
329 <conditional name="in_cond">
330 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
331 </conditional>
332 <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
333 <param name="keep_subelements" value="false"/>
334 <section name="algorithm">
335 <param name="mz_unit" value="ppm"/>
336 <param name="nr_partitions" value="100"/>
337 <section name="warp">
338 <param name="enabled" value="true"/>
339 <param name="rt_tol" value="100.0"/>
340 <param name="mz_tol" value="5.0"/>
341 <param name="max_pairwise_log_fc" value="0.5"/>
342 <param name="min_rel_cc_size" value="0.5"/>
343 <param name="max_nr_conflicts" value="0"/>
344 </section>
345 <section name="link">
346 <param name="rt_tol" value="30.0"/>
347 <param name="mz_tol" value="10.0"/>
348 <param name="charge_merging" value="Identical"/>
349 <param name="adduct_merging" value="Any"/>
350 </section>
351 <section name="distance_RT">
352 <param name="exponent" value="1.0"/>
353 <param name="weight" value="1.0"/>
354 </section>
355 <section name="distance_MZ">
356 <param name="exponent" value="2.0"/>
357 <param name="weight" value="1.0"/>
358 </section>
359 <section name="distance_intensity">
360 <param name="exponent" value="1.0"/>
361 <param name="weight" value="1.0"/>
362 <param name="log_transform" value="enabled"/>
363 </section>
364 <section name="LOWESS">
365 <param name="span" value="0.666666666666667"/>
366 <param name="num_iterations" value="3"/>
367 <param name="delta" value="-1.0"/>
368 <param name="interpolation_type" value="cspline"/>
369 <param name="extrapolation_type" value="four-point-linear"/>
370 </section>
371 </section>
372 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
373 <output name="ctd_out" ftype="xml">
374 <assert_contents>
375 <is_valid_xml/>
376 </assert_contents>
377 </output>
378 </test>
379 <!-- TOPP_FeatureLinkerUnlabeledKD_5 -->
380 <test expect_num_outputs="2">
381 <section name="adv_opts">
382 <param name="force" value="false"/>
383 <param name="test" value="true"/>
384 </section>
385 <conditional name="in_cond">
386 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
387 </conditional>
388 <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
389 <param name="keep_subelements" value="false"/>
390 <section name="algorithm">
391 <param name="mz_unit" value="ppm"/>
392 <param name="nr_partitions" value="100"/>
393 <section name="warp">
394 <param name="enabled" value="true"/>
395 <param name="rt_tol" value="100.0"/>
396 <param name="mz_tol" value="5.0"/>
397 <param name="max_pairwise_log_fc" value="0.5"/>
398 <param name="min_rel_cc_size" value="0.5"/>
399 <param name="max_nr_conflicts" value="0"/>
400 </section>
401 <section name="link">
402 <param name="rt_tol" value="30.0"/>
403 <param name="mz_tol" value="10.0"/>
404 <param name="charge_merging" value="With_charge_zero"/>
405 <param name="adduct_merging" value="Any"/>
406 </section>
407 <section name="distance_RT">
408 <param name="exponent" value="1.0"/>
409 <param name="weight" value="1.0"/>
410 </section>
411 <section name="distance_MZ">
412 <param name="exponent" value="2.0"/>
413 <param name="weight" value="1.0"/>
414 </section>
415 <section name="distance_intensity">
416 <param name="exponent" value="1.0"/>
417 <param name="weight" value="1.0"/>
418 <param name="log_transform" value="enabled"/>
419 </section>
420 <section name="LOWESS">
421 <param name="span" value="0.666666666666667"/>
422 <param name="num_iterations" value="3"/>
423 <param name="delta" value="-1.0"/>
424 <param name="interpolation_type" value="cspline"/>
425 <param name="extrapolation_type" value="four-point-linear"/>
426 </section>
427 </section>
428 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
429 <output name="ctd_out" ftype="xml">
430 <assert_contents>
431 <is_valid_xml/>
432 </assert_contents>
433 </output>
434 </test>
435 <!-- TOPP_FeatureLinkerUnlabeledKD_6 -->
436 <test expect_num_outputs="2">
437 <section name="adv_opts">
438 <param name="force" value="false"/>
439 <param name="test" value="true"/>
440 </section>
441 <conditional name="in_cond">
442 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
443 </conditional>
444 <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
445 <param name="keep_subelements" value="false"/>
446 <section name="algorithm">
447 <param name="mz_unit" value="ppm"/>
448 <param name="nr_partitions" value="100"/>
449 <section name="warp">
450 <param name="enabled" value="true"/>
451 <param name="rt_tol" value="100.0"/>
452 <param name="mz_tol" value="5.0"/>
453 <param name="max_pairwise_log_fc" value="0.5"/>
454 <param name="min_rel_cc_size" value="0.5"/>
455 <param name="max_nr_conflicts" value="0"/>
456 </section>
457 <section name="link">
458 <param name="rt_tol" value="30.0"/>
459 <param name="mz_tol" value="10.0"/>
460 <param name="charge_merging" value="Any"/>
461 <param name="adduct_merging" value="With_unknown_adducts"/>
462 </section>
463 <section name="distance_RT">
464 <param name="exponent" value="1.0"/>
465 <param name="weight" value="1.0"/>
466 </section>
467 <section name="distance_MZ">
468 <param name="exponent" value="2.0"/>
469 <param name="weight" value="1.0"/>
470 </section>
471 <section name="distance_intensity">
472 <param name="exponent" value="1.0"/>
473 <param name="weight" value="1.0"/>
474 <param name="log_transform" value="enabled"/>
475 </section>
476 <section name="LOWESS">
477 <param name="span" value="0.666666666666667"/>
478 <param name="num_iterations" value="3"/>
479 <param name="delta" value="-1.0"/>
480 <param name="interpolation_type" value="cspline"/>
481 <param name="extrapolation_type" value="four-point-linear"/>
482 </section>
483 </section>
484 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
485 <output name="ctd_out" ftype="xml">
486 <assert_contents>
487 <is_valid_xml/>
488 </assert_contents>
489 </output>
490 </test>
491 <!-- TOPP_FeatureLinkerUnlabeledKD_7 -->
492 <test expect_num_outputs="2">
493 <section name="adv_opts">
494 <param name="force" value="false"/>
495 <param name="test" value="true"/>
496 </section>
497 <conditional name="in_cond">
498 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
499 </conditional>
500 <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
501 <param name="keep_subelements" value="false"/>
502 <section name="algorithm">
503 <param name="mz_unit" value="ppm"/>
504 <param name="nr_partitions" value="100"/>
505 <section name="warp">
506 <param name="enabled" value="true"/>
507 <param name="rt_tol" value="100.0"/>
508 <param name="mz_tol" value="5.0"/>
509 <param name="max_pairwise_log_fc" value="0.5"/>
510 <param name="min_rel_cc_size" value="0.5"/>
511 <param name="max_nr_conflicts" value="0"/>
512 </section>
513 <section name="link">
514 <param name="rt_tol" value="30.0"/>
515 <param name="mz_tol" value="10.0"/>
516 <param name="charge_merging" value="Any"/>
517 <param name="adduct_merging" value="Identical"/>
518 </section>
519 <section name="distance_RT">
520 <param name="exponent" value="1.0"/>
521 <param name="weight" value="1.0"/>
522 </section>
523 <section name="distance_MZ">
524 <param name="exponent" value="2.0"/>
525 <param name="weight" value="1.0"/>
526 </section>
527 <section name="distance_intensity">
528 <param name="exponent" value="1.0"/>
529 <param name="weight" value="1.0"/>
530 <param name="log_transform" value="enabled"/>
531 </section>
532 <section name="LOWESS">
533 <param name="span" value="0.666666666666667"/>
534 <param name="num_iterations" value="3"/>
535 <param name="delta" value="-1.0"/>
536 <param name="interpolation_type" value="cspline"/>
537 <param name="extrapolation_type" value="four-point-linear"/>
538 </section>
539 </section>
540 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
541 <output name="ctd_out" ftype="xml">
542 <assert_contents>
543 <is_valid_xml/>
544 </assert_contents>
545 </output>
546 </test>
140 </tests> 547 </tests>
141 <help><![CDATA[Groups corresponding features from multiple maps. 548 <help><![CDATA[Groups corresponding features from multiple maps.
142 549
143 550
144 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerUnlabeledKD.html]]></help> 551 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledKD.html]]></help>
145 <expand macro="references"/> 552 <expand macro="references"/>
146 </tool> 553 </tool>