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comparison FeatureFinderMultiplex.xml @ 12:3098bea02bd8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:50:38 +0000
parents e8651e585689
children 5e5771b511a3
comparison
equal deleted inserted replaced
11:dff6c756eee5 12:3098bea02bd8
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.3.0"> 4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Determination of peak ratios in LC-MS data</description> 5 <description>Determination of peak ratios in LC-MS data</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> 7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FeatureFinderMultiplex 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out &&
17 #end if 23 #end if
18 #if $param_out: 24 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
19 -out $param_out 25 mkdir out_multiplets &&
20 #end if 26 #end if
21 #if $param_out_features: 27 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 -out_features $param_out_features 28 mkdir out_blacklist &&
23 #end if
24 #if $param_out_mzq:
25 -out_mzq $param_out_mzq
26 #end if 29 #end if
27 30
28 -algorithm:labels '$param_algorithm_labels' 31 ## Main program call
29 32
30 #if $param_algorithm_charge: 33 set -o pipefail &&
31 -algorithm:charge "$param_algorithm_charge" 34 @EXECUTABLE@ -write_ctd ./ &&
35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
37 -in
38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
40 -out
41 'out/output.${gxy2omsext("featurexml")}'
32 #end if 42 #end if
33 #if $param_algorithm_rt_typical: 43 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 -algorithm:rt_typical $param_algorithm_rt_typical 44 -out_multiplets
45 'out_multiplets/output.${gxy2omsext("consensusxml")}'
35 #end if 46 #end if
36 #if $param_algorithm_rt_min: 47 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -algorithm:rt_min $param_algorithm_rt_min 48 -out_blacklist
49 'out_blacklist/output.${gxy2omsext("mzml")}'
38 #end if 50 #end if
39 #if $param_algorithm_mz_tolerance: 51 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
40 -algorithm:mz_tolerance $param_algorithm_mz_tolerance 52 | tee '$stdout'
41 #end if 53 #end if
42 #if $param_algorithm_mz_unit: 54
43 -algorithm:mz_unit 55 ## Postprocessing
44 #if " " in str($param_algorithm_mz_unit): 56 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
45 "$param_algorithm_mz_unit" 57 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
46 #else
47 $param_algorithm_mz_unit
48 #end if
49 #end if 58 #end if
50 #if $param_algorithm_intensity_cutoff: 59 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
51 -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff 60 && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets'
52 #end if 61 #end if
53 #if $param_algorithm_peptide_similarity: 62 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 -algorithm:peptide_similarity $param_algorithm_peptide_similarity 63 && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist'
55 #end if 64 #end if
56 #if $param_algorithm_averagine_similarity: 65 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
57 -algorithm:averagine_similarity $param_algorithm_averagine_similarity 66 && mv '@EXECUTABLE@.ctd' '$ctd_out'
58 #end if 67 #end if]]></command>
59 #if $param_algorithm_missed_cleavages: 68 <configfiles>
60 -algorithm:missed_cleavages $param_algorithm_missed_cleavages 69 <inputs name="args_json" data_style="paths"/>
61 #end if 70 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
62 #if $adv_opts.adv_opts_selector=='advanced': 71 </configfiles>
63 #if $adv_opts.param_force:
64 -force
65 #end if
66 #if $adv_opts.param_algorithm_isotopes_per_peptide:
67 -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide"
68 #end if
69 #if $adv_opts.param_algorithm_averagine_similarity_scaling:
70 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
71 #end if
72 #if $adv_opts.param_algorithm_knock_out:
73 -algorithm:knock_out
74 #end if
75 #if $adv_opts.param_algorithm_spectrum_type:
76 -algorithm:spectrum_type
77 #if " " in str($adv_opts.param_algorithm_spectrum_type):
78 "$adv_opts.param_algorithm_spectrum_type"
79 #else
80 $adv_opts.param_algorithm_spectrum_type
81 #end if
82 #end if
83 #if $adv_opts.param_algorithm_averagine_type:
84 -algorithm:averagine_type
85 #if " " in str($adv_opts.param_algorithm_averagine_type):
86 "$adv_opts.param_algorithm_averagine_type"
87 #else
88 $adv_opts.param_algorithm_averagine_type
89 #end if
90 #end if
91 #if $adv_opts.param_labels_Arg6:
92 -labels:Arg6 $adv_opts.param_labels_Arg6
93 #end if
94 #if $adv_opts.param_labels_Arg10:
95 -labels:Arg10 $adv_opts.param_labels_Arg10
96 #end if
97 #if $adv_opts.param_labels_Lys4:
98 -labels:Lys4 $adv_opts.param_labels_Lys4
99 #end if
100 #if $adv_opts.param_labels_Lys6:
101 -labels:Lys6 $adv_opts.param_labels_Lys6
102 #end if
103 #if $adv_opts.param_labels_Lys8:
104 -labels:Lys8 $adv_opts.param_labels_Lys8
105 #end if
106 #if $adv_opts.param_labels_Leu3:
107 -labels:Leu3 $adv_opts.param_labels_Leu3
108 #end if
109 #if $adv_opts.param_labels_Dimethyl0:
110 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
111 #end if
112 #if $adv_opts.param_labels_Dimethyl4:
113 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
114 #end if
115 #if $adv_opts.param_labels_Dimethyl6:
116 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
117 #end if
118 #if $adv_opts.param_labels_Dimethyl8:
119 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
120 #end if
121 #if $adv_opts.param_labels_ICPL0:
122 -labels:ICPL0 $adv_opts.param_labels_ICPL0
123 #end if
124 #if $adv_opts.param_labels_ICPL4:
125 -labels:ICPL4 $adv_opts.param_labels_ICPL4
126 #end if
127 #if $adv_opts.param_labels_ICPL6:
128 -labels:ICPL6 $adv_opts.param_labels_ICPL6
129 #end if
130 #if $adv_opts.param_labels_ICPL10:
131 -labels:ICPL10 $adv_opts.param_labels_ICPL10
132 #end if
133 #end if
134 -threads "\${GALAXY_SLOTS:-1}"
135 ]]></command>
136 <inputs> 72 <inputs>
137 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/> 73 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
138 <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 74 <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
139 <sanitizer> 75 <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">
140 <valid initial="string.printable"> 76 <expand macro="list_string_san"/>
141 <remove value="'"/>
142 <remove value="&quot;"/>
143 </valid>
144 </sanitizer>
145 </param>
146 <param name="param_algorithm_charge" type="text" size="30" value="1:4" label="Range of charge states in the sample, i.e" help="(-charge) min charge : max charge">
147 <sanitizer>
148 <valid initial="string.printable">
149 <remove value="'"/>
150 <remove value="&quot;"/>
151 </valid>
152 </sanitizer>
153 </param>
154 <param name="param_algorithm_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)"/>
155 <param name="param_algorithm_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]" help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)"/>
156 <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns" help="(-mz_tolerance) "/>
157 <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) ">
158 <option value="Da">Da</option>
159 <option value="ppm" selected="true">ppm</option>
160 </param>
161 <param name="param_algorithm_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help="(-intensity_cutoff) "/>
162 <param name="param_algorithm_peptide_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="(-peptide_similarity) This parameter is a lower bound on their similarity"/>
163 <param name="param_algorithm_averagine_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
164 <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
165 <expand macro="advanced_options">
166 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
167 <param name="param_algorithm_isotopes_per_peptide" type="text" size="30" value="3:6" label="Range of isotopes per peptide in the sample" help="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
168 <sanitizer>
169 <valid initial="string.printable">
170 <remove value="'"/>
171 <remove value="&quot;"/>
172 </valid>
173 </sanitizer>
174 </param> 77 </param>
175 <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) 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 simulataneously. 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.)"/> 78 <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">
176 <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/> 79 <expand macro="list_string_san"/>
177 <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file"> 80 </param>
81 <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. ">
82 <expand macro="list_string_san"/>
83 </param>
84 <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.)"/>
85 <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"/>
86 <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.)"/>
87 <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=""/>
88 <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of the 'mz_tolerance' paramete" help="">
89 <option value="Da">Da</option>
90 <option value="ppm" selected="true">ppm</option>
91 <expand macro="list_string_san"/>
92 </param>
93 <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=""/>
94 <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"/>
95 <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"/>
96 <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 simulataneously. 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.)"/>
97 <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.)"/>
98 <param name="spectrum_type" argument="-algorithm:spectrum_type" display="radio" type="select" optional="false" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
178 <option value="profile">profile</option> 99 <option value="profile">profile</option>
179 <option value="centroid">centroid</option> 100 <option value="centroid">centroid</option>
180 <option value="automatic" selected="true">automatic</option> 101 <option value="automatic" selected="true">automatic</option>
102 <expand macro="list_string_san"/>
181 </param> 103 </param>
182 <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) "> 104 <param name="averagine_type" argument="-algorithm:averagine_type" display="radio" type="select" optional="false" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
183 <option value="peptide" selected="true">peptide</option> 105 <option value="peptide" selected="true">peptide</option>
184 <option value="RNA">RNA</option> 106 <option value="RNA">RNA</option>
185 <option value="DNA">DNA</option> 107 <option value="DNA">DNA</option>
108 <expand macro="list_string_san"/>
186 </param> 109 </param>
187 <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/> 110 <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.)"/>
188 <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/> 111 </section>
189 <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/> 112 <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
190 <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/> 113 <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=""/>
191 <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/> 114 <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=""/>
192 <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/> 115 <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=""/>
193 <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/> 116 <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=""/>
194 <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/> 117 <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=""/>
195 <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/> 118 <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=""/>
196 <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/> 119 <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=""/>
197 <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/> 120 <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=""/>
198 <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/> 121 <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=""/>
199 <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/> 122 <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=""/>
200 <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/> 123 <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=""/>
124 <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=""/>
125 <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=""/>
126 <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=""/>
127 </section>
128 <expand macro="adv_opts_macro">
129 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
130 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
131 <expand macro="list_string_san"/>
132 </param>
201 </expand> 133 </expand>
134 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
135 <option value="out_FLAG">out (ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866)</option>
136 <option value="out_multiplets_FLAG">out_multiplets (ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866)</option>
137 <option value="out_blacklist_FLAG">out_blacklist (ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866)</option>
138 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
139 </param>
202 </inputs> 140 </inputs>
203 <outputs> 141 <outputs>
204 <data name="param_out" format="consensusxml" label="${tool.name} on ${on_string}: consensusxml"/> 142 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
205 <data name="param_out_features" format="featurexml" label="${tool.name} on ${on_string}: featurexml"/> 143 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
206 <data name="param_out_mzq" format="mzq" label="${tool.name} on ${on_string}: mzq"/> 144 </data>
145 <data name="out_multiplets" label="${tool.name} on ${on_string}: out_multiplets" format="consensusxml">
146 <filter>OPTIONAL_OUTPUTS is not None and "out_multiplets_FLAG" in OPTIONAL_OUTPUTS</filter>
147 </data>
148 <data name="out_blacklist" label="${tool.name} on ${on_string}: out_blacklist" format="mzml">
149 <filter>OPTIONAL_OUTPUTS is not None and "out_blacklist_FLAG" in OPTIONAL_OUTPUTS</filter>
150 </data>
151 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
152 <filter>OPTIONAL_OUTPUTS is None</filter>
153 </data>
154 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
156 </data>
207 </outputs> 157 </outputs>
208 <help>Determination of peak ratios in LC-MS data 158 <tests>
159 <expand macro="autotest_FeatureFinderMultiplex"/>
160 <expand macro="manutest_FeatureFinderMultiplex"/>
161 </tests>
162 <help><![CDATA[Determination of peak ratios in LC-MS data
209 163
210 164
211 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMultiplex.html</help> 165 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMultiplex.html]]></help>
166 <expand macro="references"/>
212 </tool> 167 </tool>