Mercurial > repos > galaxyp > openms_featurefindermetabo
annotate FeatureFinderMetabo.xml @ 15:2451315543f9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:24:19 +0000 |
parents | 00080bb4299e |
children | a49dde5a836e |
rev | line source |
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2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
7
1473223a9595
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Quantitation]--> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description> |
2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token> |
2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 @EXT_FOO@ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 #import re |
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2602a6da5ad3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 |
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 ## Preprocessing |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 mkdir in && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir out && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 mkdir out_chrom && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 #end if |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 ## Main program call |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 set -o pipefail && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 @EXECUTABLE@ -write_ctd ./ && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 -in |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 -out |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 'out/output.${gxy2omsext("featurexml")}' |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 -out_chrom |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 'out_chrom/output.${gxy2omsext("mzml")}' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 #end if |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 | tee '$stdout' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 #end if |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 ## Postprocessing |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 && mv 'out_chrom/output.${gxy2omsext("mzml")}' '$out_chrom' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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46 #end if |
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47 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
21dc135961b5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 #end if]]></command> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 <configfiles> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 <inputs name="args_json" data_style="paths"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 </configfiles> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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54 <inputs> |
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55 <param argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 <section name="common" title="Common parameters for all other subsections" help="" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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59 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 </section> |
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62 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/> |
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65 <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <option value="area" selected="true">area</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 <option value="median">median</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68 <option value="max_height">max_height</option> |
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69 <expand macro="list_string_san" name="quant_method"/> |
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70 </param> |
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71 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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72 <option value="outlier" selected="true">outlier</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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73 <option value="sample_rate">sample_rate</option> |
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74 <expand macro="list_string_san" name="trace_termination_criterion"/> |
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75 </param> |
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76 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/> |
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77 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/> |
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78 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/> |
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79 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/> |
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80 </section> |
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81 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false"> |
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82 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/> |
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83 <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution"> |
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84 <option value="off">off</option> |
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85 <option value="fixed" selected="true">fixed</option> |
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86 <option value="auto">auto</option> |
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87 <expand macro="list_string_san" name="width_filtering"/> |
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88 </param> |
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89 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> |
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90 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> |
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91 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/> |
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92 </section> |
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93 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false"> |
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94 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/> |
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95 <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/> |
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96 <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/> |
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97 <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/> |
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98 <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/> |
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99 <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/> |
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100 <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="true" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device"> |
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101 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> |
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102 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> |
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103 <option value="peptides">peptides</option> |
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104 <option value="none">none</option> |
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105 <expand macro="list_string_san" name="isotope_filtering_model"/> |
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106 </param> |
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107 <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/> |
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108 <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/> |
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109 <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/> |
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110 <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/> |
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111 <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/> |
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112 <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help=""> |
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113 <expand macro="list_string_san" name="elements"/> |
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114 </param> |
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115 </section> |
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116 </section> |
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117 <expand macro="adv_opts_macro"> |
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118 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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119 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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120 <expand macro="list_string_san" name="test"/> |
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121 </param> |
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122 </expand> |
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123 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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124 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option> |
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125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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126 </param> |
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127 </inputs> |
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128 <outputs> |
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129 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
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130 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom" format="mzml"> |
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131 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter> |
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132 </data> |
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133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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135 </data> |
0
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136 </outputs> |
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137 <tests><!-- TOPP_FeatureFinderMetabo_1 --> |
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138 <test expect_num_outputs="2"> |
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139 <section name="adv_opts"> |
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140 <param name="force" value="false"/> |
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141 <param name="test" value="true"/> |
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142 </section> |
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143 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> |
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144 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
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145 <section name="algorithm"> |
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146 <section name="common"> |
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147 <param name="noise_threshold_int" value="10.0"/> |
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148 <param name="chrom_peak_snr" value="3.0"/> |
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149 <param name="chrom_fwhm" value="5.0"/> |
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150 </section> |
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151 <section name="mtd"> |
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152 <param name="mass_error_ppm" value="20.0"/> |
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153 <param name="reestimate_mt_sd" value="true"/> |
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154 <param name="quant_method" value="area"/> |
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155 <param name="trace_termination_criterion" value="outlier"/> |
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156 <param name="trace_termination_outliers" value="5"/> |
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157 <param name="min_sample_rate" value="0.5"/> |
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158 <param name="min_trace_length" value="5.0"/> |
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159 <param name="max_trace_length" value="300.0"/> |
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160 </section> |
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161 <section name="epd"> |
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162 <param name="enabled" value="true"/> |
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163 <param name="width_filtering" value="off"/> |
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164 <param name="min_fwhm" value="3.0"/> |
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165 <param name="max_fwhm" value="60.0"/> |
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166 <param name="masstrace_snr_filtering" value="false"/> |
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167 </section> |
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168 <section name="ffm"> |
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169 <param name="local_rt_range" value="10.0"/> |
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170 <param name="local_mz_range" value="6.5"/> |
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171 <param name="charge_lower_bound" value="1"/> |
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172 <param name="charge_upper_bound" value="3"/> |
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173 <param name="report_summed_ints" value="false"/> |
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174 <param name="enable_RT_filtering" value="true"/> |
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175 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> |
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176 <param name="mz_scoring_13C" value="true"/> |
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177 <param name="use_smoothed_intensities" value="true"/> |
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178 <param name="report_convex_hulls" value="false"/> |
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179 <param name="remove_single_traces" value="false"/> |
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180 <param name="mz_scoring_by_elements" value="false"/> |
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181 <param name="elements" value="CHNOPS"/> |
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182 </section> |
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183 </section> |
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184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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185 <output name="ctd_out" ftype="xml"> |
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186 <assert_contents> |
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187 <is_valid_xml/> |
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188 </assert_contents> |
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189 </output> |
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190 </test> |
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191 <!-- TOPP_FeatureFinderMetabo_2 --> |
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192 <test expect_num_outputs="2"> |
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193 <section name="adv_opts"> |
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194 <param name="force" value="false"/> |
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195 <param name="test" value="true"/> |
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196 </section> |
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197 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> |
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198 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
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199 <section name="algorithm"> |
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200 <section name="common"> |
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201 <param name="noise_threshold_int" value="100.0"/> |
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202 <param name="chrom_peak_snr" value="0.0"/> |
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203 <param name="chrom_fwhm" value="100.0"/> |
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204 </section> |
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205 <section name="mtd"> |
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206 <param name="mass_error_ppm" value="5.0"/> |
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207 <param name="reestimate_mt_sd" value="true"/> |
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208 <param name="quant_method" value="median"/> |
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209 <param name="trace_termination_criterion" value="sample_rate"/> |
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210 <param name="trace_termination_outliers" value="2"/> |
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211 <param name="min_sample_rate" value="0.01"/> |
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212 <param name="min_trace_length" value="30.0"/> |
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213 <param name="max_trace_length" value="3000.0"/> |
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214 </section> |
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215 <section name="epd"> |
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216 <param name="enabled" value="false"/> |
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217 <param name="width_filtering" value="off"/> |
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218 <param name="min_fwhm" value="10.0"/> |
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219 <param name="max_fwhm" value="80.0"/> |
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220 <param name="masstrace_snr_filtering" value="false"/> |
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221 </section> |
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222 <section name="ffm"> |
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223 <param name="local_rt_range" value="10.0"/> |
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224 <param name="local_mz_range" value="4.5"/> |
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225 <param name="charge_lower_bound" value="1"/> |
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226 <param name="charge_upper_bound" value="3"/> |
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227 <param name="report_summed_ints" value="false"/> |
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228 <param name="enable_RT_filtering" value="false"/> |
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229 <param name="isotope_filtering_model" value="none"/> |
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230 <param name="mz_scoring_13C" value="false"/> |
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231 <param name="use_smoothed_intensities" value="false"/> |
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232 <param name="report_convex_hulls" value="true"/> |
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233 <param name="remove_single_traces" value="false"/> |
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234 <param name="mz_scoring_by_elements" value="false"/> |
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235 <param name="elements" value="CHNOPS"/> |
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236 </section> |
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237 </section> |
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238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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239 <output name="ctd_out" ftype="xml"> |
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240 <assert_contents> |
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241 <is_valid_xml/> |
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242 </assert_contents> |
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243 </output> |
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244 </test> |
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245 <!-- TOPP_FeatureFinderMetabo_3 --> |
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246 <test expect_num_outputs="3"> |
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247 <section name="adv_opts"> |
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248 <param name="force" value="false"/> |
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249 <param name="test" value="true"/> |
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250 </section> |
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251 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> |
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252 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
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253 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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254 <section name="algorithm"> |
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255 <section name="common"> |
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256 <param name="noise_threshold_int" value="10.0"/> |
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257 <param name="chrom_peak_snr" value="3.0"/> |
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258 <param name="chrom_fwhm" value="5.0"/> |
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259 </section> |
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260 <section name="mtd"> |
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261 <param name="mass_error_ppm" value="5.0"/> |
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262 <param name="reestimate_mt_sd" value="true"/> |
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263 <param name="quant_method" value="area"/> |
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264 <param name="trace_termination_criterion" value="outlier"/> |
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265 <param name="trace_termination_outliers" value="5"/> |
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266 <param name="min_sample_rate" value="0.5"/> |
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267 <param name="min_trace_length" value="5.0"/> |
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268 <param name="max_trace_length" value="-1.0"/> |
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269 </section> |
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270 <section name="epd"> |
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271 <param name="enabled" value="true"/> |
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272 <param name="width_filtering" value="fixed"/> |
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273 <param name="min_fwhm" value="3.0"/> |
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274 <param name="max_fwhm" value="60.0"/> |
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275 <param name="masstrace_snr_filtering" value="false"/> |
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276 </section> |
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277 <section name="ffm"> |
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278 <param name="local_rt_range" value="10.0"/> |
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279 <param name="local_mz_range" value="6.5"/> |
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280 <param name="charge_lower_bound" value="1"/> |
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281 <param name="charge_upper_bound" value="3"/> |
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282 <param name="report_summed_ints" value="false"/> |
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283 <param name="enable_RT_filtering" value="true"/> |
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284 <param name="isotope_filtering_model" value="none"/> |
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285 <param name="mz_scoring_13C" value="true"/> |
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286 <param name="use_smoothed_intensities" value="true"/> |
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287 <param name="report_convex_hulls" value="true"/> |
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288 <param name="remove_single_traces" value="false"/> |
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289 <param name="mz_scoring_by_elements" value="false"/> |
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290 <param name="elements" value="CHNOPS"/> |
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291 </section> |
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292 </section> |
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293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> |
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294 <output name="ctd_out" ftype="xml"> |
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295 <assert_contents> |
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296 <is_valid_xml/> |
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297 </assert_contents> |
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298 </output> |
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299 </test> |
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300 <!-- TOPP_FeatureFinderMetabo_4 --> |
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301 <test expect_num_outputs="3"> |
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302 <section name="adv_opts"> |
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303 <param name="force" value="false"/> |
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304 <param name="test" value="true"/> |
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305 </section> |
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306 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> |
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307 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
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308 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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309 <section name="algorithm"> |
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310 <section name="common"> |
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311 <param name="noise_threshold_int" value="10.0"/> |
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312 <param name="chrom_peak_snr" value="3.0"/> |
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313 <param name="chrom_fwhm" value="5.0"/> |
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314 </section> |
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315 <section name="mtd"> |
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316 <param name="mass_error_ppm" value="5.0"/> |
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317 <param name="reestimate_mt_sd" value="true"/> |
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318 <param name="quant_method" value="area"/> |
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319 <param name="trace_termination_criterion" value="outlier"/> |
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320 <param name="trace_termination_outliers" value="5"/> |
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321 <param name="min_sample_rate" value="0.5"/> |
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322 <param name="min_trace_length" value="5.0"/> |
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323 <param name="max_trace_length" value="-1.0"/> |
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324 </section> |
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325 <section name="epd"> |
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326 <param name="enabled" value="true"/> |
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327 <param name="width_filtering" value="fixed"/> |
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328 <param name="min_fwhm" value="3.0"/> |
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329 <param name="max_fwhm" value="60.0"/> |
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330 <param name="masstrace_snr_filtering" value="false"/> |
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331 </section> |
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332 <section name="ffm"> |
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333 <param name="local_rt_range" value="10.0"/> |
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334 <param name="local_mz_range" value="6.5"/> |
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335 <param name="charge_lower_bound" value="1"/> |
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336 <param name="charge_upper_bound" value="3"/> |
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337 <param name="report_summed_ints" value="false"/> |
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338 <param name="enable_RT_filtering" value="true"/> |
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339 <param name="isotope_filtering_model" value="none"/> |
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340 <param name="mz_scoring_13C" value="true"/> |
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341 <param name="use_smoothed_intensities" value="true"/> |
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342 <param name="report_convex_hulls" value="true"/> |
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343 <param name="remove_single_traces" value="true"/> |
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344 <param name="mz_scoring_by_elements" value="false"/> |
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345 <param name="elements" value="CHNOPS"/> |
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346 </section> |
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347 </section> |
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348 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> |
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349 <output name="ctd_out" ftype="xml"> |
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350 <assert_contents> |
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351 <is_valid_xml/> |
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352 </assert_contents> |
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353 </output> |
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354 </test> |
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355 <!-- TOPP_FeatureFinderMetabo_5 --> |
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356 <test expect_num_outputs="2"> |
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357 <section name="adv_opts"> |
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358 <param name="force" value="false"/> |
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359 <param name="test" value="true"/> |
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360 </section> |
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361 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> |
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362 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
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363 <section name="algorithm"> |
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364 <section name="common"> |
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365 <param name="noise_threshold_int" value="10.0"/> |
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366 <param name="chrom_peak_snr" value="3.0"/> |
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367 <param name="chrom_fwhm" value="5.0"/> |
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368 </section> |
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369 <section name="mtd"> |
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370 <param name="mass_error_ppm" value="20.0"/> |
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371 <param name="reestimate_mt_sd" value="true"/> |
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372 <param name="quant_method" value="max_height"/> |
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373 <param name="trace_termination_criterion" value="outlier"/> |
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374 <param name="trace_termination_outliers" value="5"/> |
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375 <param name="min_sample_rate" value="0.5"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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376 <param name="min_trace_length" value="5.0"/> |
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377 <param name="max_trace_length" value="300.0"/> |
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378 </section> |
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379 <section name="epd"> |
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380 <param name="enabled" value="true"/> |
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381 <param name="width_filtering" value="off"/> |
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382 <param name="min_fwhm" value="3.0"/> |
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383 <param name="max_fwhm" value="60.0"/> |
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384 <param name="masstrace_snr_filtering" value="false"/> |
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385 </section> |
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386 <section name="ffm"> |
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387 <param name="local_rt_range" value="10.0"/> |
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388 <param name="local_mz_range" value="6.5"/> |
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389 <param name="charge_lower_bound" value="1"/> |
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390 <param name="charge_upper_bound" value="3"/> |
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391 <param name="report_summed_ints" value="false"/> |
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392 <param name="enable_RT_filtering" value="true"/> |
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393 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> |
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394 <param name="mz_scoring_13C" value="true"/> |
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395 <param name="use_smoothed_intensities" value="true"/> |
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396 <param name="report_convex_hulls" value="false"/> |
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397 <param name="remove_single_traces" value="false"/> |
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398 <param name="mz_scoring_by_elements" value="false"/> |
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399 <param name="elements" value="CHNOPS"/> |
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400 </section> |
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401 </section> |
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402 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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403 <output name="ctd_out" ftype="xml"> |
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404 <assert_contents> |
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405 <is_valid_xml/> |
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406 </assert_contents> |
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407 </output> |
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408 </test> |
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409 </tests> |
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410 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. |
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411 |
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412 |
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413 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help> |
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414 <expand macro="references"/> |
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415 </tool> |