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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 21:36:30 +0000
parents 9876bda3ec53
children
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16:9876bda3ec53 17:c9b2a5022d9e
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: [Quantitation]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Determination of peak ratios in LC-MS data</description> 4 <description>Determination of peak ratios in LC-MS data</description>
6 <macros> 5 <macros>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 18 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
20 mkdir out && 19 mkdir out &&
21 #end if 20 #end if
22 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_multiplets && 22 mkdir out_multiplets &&
66 <configfiles> 65 <configfiles>
67 <inputs name="args_json" data_style="paths"/> 66 <inputs name="args_json" data_style="paths"/>
68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 67 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
69 </configfiles> 68 </configfiles>
70 <inputs> 69 <inputs>
71 <param argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/> 70 <param argument="-in" type="data" format="mzml" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
72 <section name="algorithm" title="algorithmic parameters" help="" expanded="false"> 71 <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
73 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 72 <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
74 <expand macro="list_string_san" name="labels"/> 73 <expand macro="list_string_san" name="labels"/>
75 </param> 74 </param>
76 <param name="charge" argument="-algorithm:charge" type="text" optional="true" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge"> 75 <param name="charge" argument="-algorithm:charge" type="text" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge">
77 <expand macro="list_string_san" name="charge"/> 76 <expand macro="list_string_san" name="charge"/>
78 </param> 77 </param>
79 <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" optional="true" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. "> 78 <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
80 <expand macro="list_string_san" name="isotopes_per_peptide"/> 79 <expand macro="list_string_san" name="isotopes_per_peptide"/>
81 </param> 80 </param>
82 <param name="rt_typical" argument="-algorithm:rt_typical" type="float" optional="true" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/> 81 <param name="rt_typical" argument="-algorithm:rt_typical" type="float" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/>
83 <param name="rt_band" argument="-algorithm:rt_band" type="float" optional="true" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/> 82 <param name="rt_band" argument="-algorithm:rt_band" type="float" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
84 <param name="rt_min" argument="-algorithm:rt_min" type="float" optional="true" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/> 83 <param name="rt_min" argument="-algorithm:rt_min" type="float" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
85 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" optional="true" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/> 84 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
86 <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" label="Unit of the 'mz_tolerance' paramete" help=""> 85 <param name="mz_unit" argument="-algorithm:mz_unit" type="select" label="Unit of the 'mz_tolerance' paramete" help="">
87 <option value="Da">Da</option> 86 <option value="Da">Da</option>
88 <option value="ppm" selected="true">ppm</option> 87 <option value="ppm" selected="true">ppm</option>
89 <expand macro="list_string_san" name="mz_unit"/> 88 <expand macro="list_string_san" name="mz_unit"/>
90 </param> 89 </param>
91 <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" optional="true" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/> 90 <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/>
92 <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/> 91 <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/>
93 <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/> 92 <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
94 <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/> 93 <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
95 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> 94 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
96 <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="true" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file"> 95 <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
97 <option value="profile">profile</option> 96 <option value="profile">profile</option>
98 <option value="centroid">centroid</option> 97 <option value="centroid">centroid</option>
99 <option value="automatic" selected="true">automatic</option> 98 <option value="automatic" selected="true">automatic</option>
100 <expand macro="list_string_san" name="spectrum_type"/> 99 <expand macro="list_string_san" name="spectrum_type"/>
101 </param> 100 </param>
102 <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="true" label="The type of averagine to use, currently RNA, DNA or peptide" help=""> 101 <param name="averagine_type" argument="-algorithm:averagine_type" type="select" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
103 <option value="peptide" selected="true">peptide</option> 102 <option value="peptide" selected="true">peptide</option>
104 <option value="RNA">RNA</option> 103 <option value="RNA">RNA</option>
105 <option value="DNA">DNA</option> 104 <option value="DNA">DNA</option>
106 <expand macro="list_string_san" name="averagine_type"/> 105 <expand macro="list_string_san" name="averagine_type"/>
107 </param> 106 </param>
108 <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/> 107 <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/>
109 </section> 108 </section>
110 <section name="labels" title="mass shifts for all possible labels" help="" expanded="false"> 109 <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
111 <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> 110 <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
112 <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> 111 <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
113 <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> 112 <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
114 <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> 113 <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
115 <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> 114 <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
116 <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> 115 <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
117 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> 116 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
118 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> 117 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
119 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> 118 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
120 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> 119 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
121 <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> 120 <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
122 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> 121 <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
123 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> 122 <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
124 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> 123 <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
125 </section> 124 </section>
126 <expand macro="adv_opts_macro"> 125 <expand macro="adv_opts_macro">
127 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 126 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
128 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 127 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
129 <expand macro="list_string_san" name="test"/> 128 <expand macro="list_string_san" name="test"/>
130 </param> 129 </param>
131 </expand> 130 </expand>
132 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 131 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
133 <option value="out_FLAG">out (Output file containing the individual peptide features)</option> 132 <option value="out_FLAG">out (Output file containing the individual peptide features)</option>
151 </data> 150 </data>
152 <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">
153 <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>
154 </data> 153 </data>
155 </outputs> 154 </outputs>
156 <tests><!-- TOPP_FeatureFinderMultiplex_1 --> 155 <tests>
156 <!-- TOPP_FeatureFinderMultiplex_1 -->
157 <test expect_num_outputs="3"> 157 <test expect_num_outputs="3">
158 <section name="adv_opts"> 158 <section name="adv_opts">
159 <param name="force" value="false"/> 159 <param name="force" value="false"/>
160 <param name="test" value="true"/> 160 <param name="test" value="true"/>
161 </section> 161 </section>
162 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> 162 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
163 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 163 <output name="out" value="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
164 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 164 <output name="out_multiplets" value="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
165 <section name="algorithm"> 165 <section name="algorithm">
166 <param name="labels" value="[Dimethyl0][Dimethyl8]"/> 166 <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
167 <param name="charge" value="1:4"/> 167 <param name="charge" value="1:4"/>
168 <param name="isotopes_per_peptide" value="3:6"/> 168 <param name="isotopes_per_peptide" value="3:6"/>
169 <param name="rt_typical" value="90.0"/> 169 <param name="rt_typical" value="90.0"/>
200 <output name="ctd_out" ftype="xml"> 200 <output name="ctd_out" ftype="xml">
201 <assert_contents> 201 <assert_contents>
202 <is_valid_xml/> 202 <is_valid_xml/>
203 </assert_contents> 203 </assert_contents>
204 </output> 204 </output>
205 <assert_stdout>
206 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
207 </assert_stdout>
205 </test> 208 </test>
206 <!-- TOPP_FeatureFinderMultiplex_2 --> 209 <!-- TOPP_FeatureFinderMultiplex_2 -->
207 <test expect_num_outputs="3"> 210 <test expect_num_outputs="3">
208 <section name="adv_opts"> 211 <section name="adv_opts">
209 <param name="force" value="false"/> 212 <param name="force" value="false"/>
210 <param name="test" value="true"/> 213 <param name="test" value="true"/>
211 </section> 214 </section>
212 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> 215 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
213 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 216 <output name="out" value="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
214 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 217 <output name="out_multiplets" value="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
215 <section name="algorithm"> 218 <section name="algorithm">
216 <param name="labels" value="[][Lys8,Arg10]"/> 219 <param name="labels" value="[][Lys8,Arg10]"/>
217 <param name="charge" value="1:4"/> 220 <param name="charge" value="1:4"/>
218 <param name="isotopes_per_peptide" value="3:6"/> 221 <param name="isotopes_per_peptide" value="3:6"/>
219 <param name="rt_typical" value="40.0"/> 222 <param name="rt_typical" value="40.0"/>
250 <output name="ctd_out" ftype="xml"> 253 <output name="ctd_out" ftype="xml">
251 <assert_contents> 254 <assert_contents>
252 <is_valid_xml/> 255 <is_valid_xml/>
253 </assert_contents> 256 </assert_contents>
254 </output> 257 </output>
258 <assert_stdout>
259 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
260 </assert_stdout>
255 </test> 261 </test>
256 <!-- TOPP_FeatureFinderMultiplex_3 --> 262 <!-- TOPP_FeatureFinderMultiplex_3 -->
257 <test expect_num_outputs="3"> 263 <test expect_num_outputs="3">
258 <section name="adv_opts"> 264 <section name="adv_opts">
259 <param name="force" value="false"/> 265 <param name="force" value="false"/>
260 <param name="test" value="true"/> 266 <param name="test" value="true"/>
261 </section> 267 </section>
262 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> 268 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
263 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 269 <output name="out" value="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
264 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 270 <output name="out_multiplets" value="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
265 <section name="algorithm"> 271 <section name="algorithm">
266 <param name="labels" value="[]"/> 272 <param name="labels" value="[]"/>
267 <param name="charge" value="5:15"/> 273 <param name="charge" value="5:15"/>
268 <param name="isotopes_per_peptide" value="5:10"/> 274 <param name="isotopes_per_peptide" value="5:10"/>
269 <param name="rt_typical" value="45.0"/> 275 <param name="rt_typical" value="45.0"/>
300 <output name="ctd_out" ftype="xml"> 306 <output name="ctd_out" ftype="xml">
301 <assert_contents> 307 <assert_contents>
302 <is_valid_xml/> 308 <is_valid_xml/>
303 </assert_contents> 309 </assert_contents>
304 </output> 310 </output>
311 <assert_stdout>
312 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
313 </assert_stdout>
305 </test> 314 </test>
306 <!-- TOPP_FeatureFinderMultiplex_4 --> 315 <!-- TOPP_FeatureFinderMultiplex_4 -->
307 <test expect_num_outputs="3"> 316 <test expect_num_outputs="3">
308 <section name="adv_opts"> 317 <section name="adv_opts">
309 <param name="force" value="false"/> 318 <param name="force" value="false"/>
310 <param name="test" value="true"/> 319 <param name="test" value="true"/>
311 </section> 320 </section>
312 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> 321 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
313 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 322 <output name="out" value="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
314 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 323 <output name="out_multiplets" value="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
315 <section name="algorithm"> 324 <section name="algorithm">
316 <param name="labels" value="[]"/> 325 <param name="labels" value="[]"/>
317 <param name="charge" value="5:15"/> 326 <param name="charge" value="5:15"/>
318 <param name="isotopes_per_peptide" value="5:10"/> 327 <param name="isotopes_per_peptide" value="5:10"/>
319 <param name="rt_typical" value="45.0"/> 328 <param name="rt_typical" value="45.0"/>
350 <output name="ctd_out" ftype="xml"> 359 <output name="ctd_out" ftype="xml">
351 <assert_contents> 360 <assert_contents>
352 <is_valid_xml/> 361 <is_valid_xml/>
353 </assert_contents> 362 </assert_contents>
354 </output> 363 </output>
364 <assert_stdout>
365 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
366 </assert_stdout>
355 </test> 367 </test>
356 <!-- TOPP_FeatureFinderMultiplex_5 --> 368 <!-- TOPP_FeatureFinderMultiplex_5 -->
357 <test expect_num_outputs="3"> 369 <test expect_num_outputs="3">
358 <section name="adv_opts"> 370 <section name="adv_opts">
359 <param name="force" value="false"/> 371 <param name="force" value="false"/>
360 <param name="test" value="true"/> 372 <param name="test" value="true"/>
361 </section> 373 </section>
362 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> 374 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
363 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 375 <output name="out" value="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
364 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 376 <output name="out_multiplets" value="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
365 <section name="algorithm"> 377 <section name="algorithm">
366 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> 378 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
367 <param name="charge" value="1:5"/> 379 <param name="charge" value="1:5"/>
368 <param name="isotopes_per_peptide" value="3:6"/> 380 <param name="isotopes_per_peptide" value="3:6"/>
369 <param name="rt_typical" value="50.0"/> 381 <param name="rt_typical" value="50.0"/>
400 <output name="ctd_out" ftype="xml"> 412 <output name="ctd_out" ftype="xml">
401 <assert_contents> 413 <assert_contents>
402 <is_valid_xml/> 414 <is_valid_xml/>
403 </assert_contents> 415 </assert_contents>
404 </output> 416 </output>
417 <assert_stdout>
418 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
419 </assert_stdout>
405 </test> 420 </test>
406 <!-- TOPP_FeatureFinderMultiplex_6 --> 421 <!-- TOPP_FeatureFinderMultiplex_6 -->
407 <test expect_num_outputs="3"> 422 <test expect_num_outputs="3">
408 <section name="adv_opts"> 423 <section name="adv_opts">
409 <param name="force" value="false"/> 424 <param name="force" value="false"/>
410 <param name="test" value="true"/> 425 <param name="test" value="true"/>
411 </section> 426 </section>
412 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> 427 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
413 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 428 <output name="out" value="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
414 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 429 <output name="out_multiplets" value="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
415 <section name="algorithm"> 430 <section name="algorithm">
416 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> 431 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
417 <param name="charge" value="1:5"/> 432 <param name="charge" value="1:5"/>
418 <param name="isotopes_per_peptide" value="3:6"/> 433 <param name="isotopes_per_peptide" value="3:6"/>
419 <param name="rt_typical" value="50.0"/> 434 <param name="rt_typical" value="50.0"/>
450 <output name="ctd_out" ftype="xml"> 465 <output name="ctd_out" ftype="xml">
451 <assert_contents> 466 <assert_contents>
452 <is_valid_xml/> 467 <is_valid_xml/>
453 </assert_contents> 468 </assert_contents>
454 </output> 469 </output>
470 <assert_stdout>
471 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
472 </assert_stdout>
455 </test> 473 </test>
456 <!-- TOPP_FeatureFinderMultiplex_7 --> 474 <!-- TOPP_FeatureFinderMultiplex_7 -->
457 <test expect_num_outputs="3"> 475 <test expect_num_outputs="3">
458 <section name="adv_opts"> 476 <section name="adv_opts">
459 <param name="force" value="false"/> 477 <param name="force" value="false"/>
460 <param name="test" value="true"/> 478 <param name="test" value="true"/>
461 </section> 479 </section>
462 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> 480 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
463 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 481 <output name="out" value="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
464 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 482 <output name="out_multiplets" value="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
465 <section name="algorithm"> 483 <section name="algorithm">
466 <param name="labels" value="[][Dimethyl4]"/> 484 <param name="labels" value="[][Dimethyl4]"/>
467 <param name="charge" value="1:4"/> 485 <param name="charge" value="1:4"/>
468 <param name="isotopes_per_peptide" value="3:6"/> 486 <param name="isotopes_per_peptide" value="3:6"/>
469 <param name="rt_typical" value="40.0"/> 487 <param name="rt_typical" value="40.0"/>
500 <output name="ctd_out" ftype="xml"> 518 <output name="ctd_out" ftype="xml">
501 <assert_contents> 519 <assert_contents>
502 <is_valid_xml/> 520 <is_valid_xml/>
503 </assert_contents> 521 </assert_contents>
504 </output> 522 </output>
523 <assert_stdout>
524 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
525 </assert_stdout>
505 </test> 526 </test>
506 <!-- TOPP_FeatureFinderMultiplex_8 --> 527 <!-- TOPP_FeatureFinderMultiplex_8 -->
507 <test expect_num_outputs="3"> 528 <test expect_num_outputs="3">
508 <section name="adv_opts"> 529 <section name="adv_opts">
509 <param name="force" value="false"/> 530 <param name="force" value="false"/>
510 <param name="test" value="true"/> 531 <param name="test" value="true"/>
511 </section> 532 </section>
512 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> 533 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
513 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 534 <output name="out" value="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
514 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 535 <output name="out_multiplets" value="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
515 <section name="algorithm"> 536 <section name="algorithm">
516 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> 537 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
517 <param name="charge" value="1:7"/> 538 <param name="charge" value="1:7"/>
518 <param name="isotopes_per_peptide" value="3:8"/> 539 <param name="isotopes_per_peptide" value="3:8"/>
519 <param name="rt_typical" value="50.0"/> 540 <param name="rt_typical" value="50.0"/>
550 <output name="ctd_out" ftype="xml"> 571 <output name="ctd_out" ftype="xml">
551 <assert_contents> 572 <assert_contents>
552 <is_valid_xml/> 573 <is_valid_xml/>
553 </assert_contents> 574 </assert_contents>
554 </output> 575 </output>
576 <assert_stdout>
577 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
578 </assert_stdout>
555 </test> 579 </test>
556 <!-- TOPP_FeatureFinderMultiplex_9 --> 580 <!-- TOPP_FeatureFinderMultiplex_9 -->
557 <test expect_num_outputs="3"> 581 <test expect_num_outputs="3">
558 <section name="adv_opts"> 582 <section name="adv_opts">
559 <param name="force" value="false"/> 583 <param name="force" value="false"/>
560 <param name="test" value="true"/> 584 <param name="test" value="true"/>
561 </section> 585 </section>
562 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> 586 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
563 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 587 <output name="out" value="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
564 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 588 <output name="out_multiplets" value="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
565 <section name="algorithm"> 589 <section name="algorithm">
566 <param name="labels" value="[0][6.03705]"/> 590 <param name="labels" value="[0][6.03705]"/>
567 <param name="charge" value="2:8"/> 591 <param name="charge" value="2:8"/>
568 <param name="isotopes_per_peptide" value="3:8"/> 592 <param name="isotopes_per_peptide" value="3:8"/>
569 <param name="rt_typical" value="40.0"/> 593 <param name="rt_typical" value="40.0"/>
600 <output name="ctd_out" ftype="xml"> 624 <output name="ctd_out" ftype="xml">
601 <assert_contents> 625 <assert_contents>
602 <is_valid_xml/> 626 <is_valid_xml/>
603 </assert_contents> 627 </assert_contents>
604 </output> 628 </output>
629 <assert_stdout>
630 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
631 </assert_stdout>
605 </test> 632 </test>
606 <!-- TOPP_FeatureFinderMultiplex_10 --> 633 <!-- TOPP_FeatureFinderMultiplex_10 -->
607 <test expect_num_outputs="3"> 634 <test expect_num_outputs="3">
608 <section name="adv_opts"> 635 <section name="adv_opts">
609 <param name="force" value="false"/> 636 <param name="force" value="false"/>
610 <param name="test" value="true"/> 637 <param name="test" value="true"/>
611 </section> 638 </section>
612 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> 639 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
613 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 640 <output name="out" value="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
614 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 641 <output name="out_multiplets" value="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
615 <section name="algorithm"> 642 <section name="algorithm">
616 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> 643 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
617 <param name="charge" value="1:7"/> 644 <param name="charge" value="1:7"/>
618 <param name="isotopes_per_peptide" value="3:6"/> 645 <param name="isotopes_per_peptide" value="3:6"/>
619 <param name="rt_typical" value="50.0"/> 646 <param name="rt_typical" value="50.0"/>
650 <output name="ctd_out" ftype="xml"> 677 <output name="ctd_out" ftype="xml">
651 <assert_contents> 678 <assert_contents>
652 <is_valid_xml/> 679 <is_valid_xml/>
653 </assert_contents> 680 </assert_contents>
654 </output> 681 </output>
682 <assert_stdout>
683 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
684 </assert_stdout>
655 </test> 685 </test>
656 <!-- TOPP_FeatureFinderMultiplex_11 --> 686 <!-- TOPP_FeatureFinderMultiplex_11 -->
657 <test expect_num_outputs="2"> 687 <test expect_num_outputs="2">
658 <section name="adv_opts"> 688 <section name="adv_opts">
659 <param name="force" value="false"/> 689 <param name="force" value="false"/>
660 <param name="test" value="true"/> 690 <param name="test" value="true"/>
661 </section> 691 </section>
662 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> 692 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
663 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 693 <output name="out" value="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
664 <section name="algorithm"> 694 <section name="algorithm">
665 <param name="labels" value="[]"/> 695 <param name="labels" value="[]"/>
666 <param name="charge" value="1:4"/> 696 <param name="charge" value="1:4"/>
667 <param name="isotopes_per_peptide" value="3:6"/> 697 <param name="isotopes_per_peptide" value="3:6"/>
668 <param name="rt_typical" value="1e-05"/> 698 <param name="rt_typical" value="1e-05"/>
699 <output name="ctd_out" ftype="xml"> 729 <output name="ctd_out" ftype="xml">
700 <assert_contents> 730 <assert_contents>
701 <is_valid_xml/> 731 <is_valid_xml/>
702 </assert_contents> 732 </assert_contents>
703 </output> 733 </output>
734 <assert_stdout>
735 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
736 </assert_stdout>
704 </test> 737 </test>
705 </tests> 738 </tests>
706 <help><![CDATA[Determination of peak ratios in LC-MS data 739 <help><![CDATA[Determination of peak ratios in LC-MS data
707 740
708 741
709 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMultiplex.html]]></help> 742 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMultiplex.html]]></help>
710 <expand macro="references"/> 743 <expand macro="references"/>
711 </tool> 744 </tool>