Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher
annotate OpenSwathMzMLFileCacher.xml @ 13:f82b320ceb90 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:04:12 +0000 |
| parents | fc775d5aa321 |
| children |
| rev | line source |
|---|---|
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5a7e590eb955
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'?> |
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e1c2ee148254
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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22820a211fe8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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3 <!--Proposed Tool Section: [Targeted Experiments]--> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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6 <macros> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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8 <import>macros.xml</import> |
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5a7e590eb955
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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9
e7c43d17e3dc
"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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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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11 <expand macro="stdio"/> |
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e7c43d17e3dc
"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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e7c43d17e3dc
"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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e7c43d17e3dc
"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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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 ## Preprocessing |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 mkdir in && |
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e7c43d17e3dc
"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)' && |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir out && |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 ## Main program call |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 set -o pipefail && |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 @EXECUTABLE@ -write_ctd ./ && |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 -in |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 -out |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 'out/output.${out_type}' |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 ## Postprocessing |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 && mv 'out/output.${out_type}' '$out' |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 #end if]]></command> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 <configfiles> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 <inputs name="args_json" data_style="paths"/> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 </configfiles> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 <inputs> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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42 <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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43 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense"> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 <option value="mzML">mzml</option> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 <option value="sqMass">sqmass</option> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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46 <expand macro="list_string_san" name="out_type"/> |
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22820a211fe8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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47 </param> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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48 <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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49 <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" 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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50 <expand macro="adv_opts_macro"> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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51 <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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52 <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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53 <param argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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56 <expand macro="list_string_san" name="test"/> |
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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 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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58 </expand> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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62 </inputs> |
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5a7e590eb955
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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63 <outputs> |
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64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"> |
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65 <change_format> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <when input="out_type" value="sqMass" format="sqmass"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 </change_format> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68 </data> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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e7c43d17e3dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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71 </data> |
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0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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72 </outputs> |
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13
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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73 <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 --> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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74 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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75 <section name="adv_opts"> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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76 <param name="lossy_mass_accuracy" value="-1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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77 <param name="process_lowmemory" value="false"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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78 <param name="lowmem_batchsize" value="500"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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79 <param name="force" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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80 <param name="test" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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81 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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82 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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83 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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84 <param name="out_type" value="mzML"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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85 <param name="lossy_compression" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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86 <param name="full_meta" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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88 <output name="ctd_out" ftype="xml"> |
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89 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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90 <is_valid_xml/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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91 </assert_contents> |
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92 </output> |
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93 </test> |
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94 <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 --> |
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95 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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96 <section name="adv_opts"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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97 <param name="lossy_mass_accuracy" value="-1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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98 <param name="process_lowmemory" value="false"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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99 <param name="lowmem_batchsize" value="500"/> |
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f82b320ceb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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100 <param name="force" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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101 <param name="test" value="true"/> |
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102 </section> |
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103 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> |
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104 <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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105 <param name="out_type" value="mzML"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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106 <param name="lossy_compression" value="true"/> |
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107 <param name="full_meta" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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109 <output name="ctd_out" ftype="xml"> |
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110 <assert_contents> |
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111 <is_valid_xml/> |
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112 </assert_contents> |
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113 </output> |
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114 </test> |
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115 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 --> |
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116 <test expect_num_outputs="2"> |
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117 <section name="adv_opts"> |
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118 <param name="lossy_mass_accuracy" value="0.0001"/> |
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119 <param name="process_lowmemory" value="false"/> |
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120 <param name="lowmem_batchsize" value="500"/> |
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121 <param name="force" value="false"/> |
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122 <param name="test" value="true"/> |
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123 </section> |
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124 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> |
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125 <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> |
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126 <param name="out_type" value="sqMass"/> |
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127 <param name="lossy_compression" value="true"/> |
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128 <param name="full_meta" value="true"/> |
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129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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130 <output name="ctd_out" ftype="xml"> |
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131 <assert_contents> |
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132 <is_valid_xml/> |
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133 </assert_contents> |
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134 </output> |
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135 </test> |
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136 <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 --> |
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137 <test expect_num_outputs="2"> |
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138 <section name="adv_opts"> |
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139 <param name="lossy_mass_accuracy" value="-1.0"/> |
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140 <param name="process_lowmemory" value="false"/> |
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141 <param name="lowmem_batchsize" value="500"/> |
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142 <param name="force" value="false"/> |
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143 <param name="test" value="true"/> |
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144 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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145 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> |
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146 <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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f82b320ceb90
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147 <param name="out_type" value="mzML"/> |
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148 <param name="lossy_compression" value="true"/> |
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149 <param name="full_meta" value="true"/> |
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150 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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151 <output name="ctd_out" ftype="xml"> |
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152 <assert_contents> |
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153 <is_valid_xml/> |
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154 </assert_contents> |
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155 </output> |
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156 </test> |
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157 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 --> |
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158 <test expect_num_outputs="2"> |
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159 <section name="adv_opts"> |
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160 <param name="lossy_mass_accuracy" value="-1.0"/> |
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161 <param name="process_lowmemory" value="false"/> |
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162 <param name="lowmem_batchsize" value="500"/> |
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163 <param name="force" value="false"/> |
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164 <param name="test" value="true"/> |
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165 </section> |
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166 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> |
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167 <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/> |
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168 <param name="out_type" value="sqMass"/> |
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169 <param name="lossy_compression" value="true"/> |
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170 <param name="full_meta" value="true"/> |
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171 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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172 <output name="ctd_out" ftype="xml"> |
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173 <assert_contents> |
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174 <is_valid_xml/> |
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175 </assert_contents> |
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176 </output> |
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177 </test> |
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178 <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 --> |
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179 <test expect_num_outputs="2"> |
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180 <section name="adv_opts"> |
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181 <param name="lossy_mass_accuracy" value="-1.0"/> |
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182 <param name="process_lowmemory" value="false"/> |
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183 <param name="lowmem_batchsize" value="500"/> |
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184 <param name="force" value="false"/> |
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185 <param name="test" value="true"/> |
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186 </section> |
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187 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> |
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188 <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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189 <param name="out_type" value="mzML"/> |
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190 <param name="lossy_compression" value="true"/> |
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191 <param name="full_meta" value="true"/> |
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192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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193 <output name="ctd_out" ftype="xml"> |
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194 <assert_contents> |
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195 <is_valid_xml/> |
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196 </assert_contents> |
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197 </output> |
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198 </test> |
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199 <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 --> |
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200 <test expect_num_outputs="2"> |
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201 <section name="adv_opts"> |
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202 <param name="lossy_mass_accuracy" value="-1.0"/> |
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203 <param name="process_lowmemory" value="true"/> |
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204 <param name="lowmem_batchsize" value="500"/> |
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205 <param name="force" value="false"/> |
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206 <param name="test" value="true"/> |
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207 </section> |
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208 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> |
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209 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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210 <param name="out_type" value="mzML"/> |
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211 <param name="lossy_compression" value="true"/> |
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212 <param name="full_meta" value="true"/> |
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213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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214 <output name="ctd_out" ftype="xml"> |
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215 <assert_contents> |
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216 <is_valid_xml/> |
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217 </assert_contents> |
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218 </output> |
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219 </test> |
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220 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 --> |
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221 <test expect_num_outputs="2"> |
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222 <section name="adv_opts"> |
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223 <param name="lossy_mass_accuracy" value="-1.0"/> |
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224 <param name="process_lowmemory" value="false"/> |
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225 <param name="lowmem_batchsize" value="500"/> |
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226 <param name="force" value="false"/> |
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227 <param name="test" value="true"/> |
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228 </section> |
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229 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> |
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230 <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> |
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231 <param name="out_type" value="mzML"/> |
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232 <param name="lossy_compression" value="true"/> |
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233 <param name="full_meta" value="true"/> |
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234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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235 <output name="ctd_out" ftype="xml"> |
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236 <assert_contents> |
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237 <is_valid_xml/> |
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238 </assert_contents> |
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239 </output> |
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240 </test> |
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241 <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 --> |
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242 <test expect_num_outputs="2"> |
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243 <section name="adv_opts"> |
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244 <param name="lossy_mass_accuracy" value="-1.0"/> |
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245 <param name="process_lowmemory" value="false"/> |
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246 <param name="lowmem_batchsize" value="500"/> |
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247 <param name="force" value="false"/> |
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248 <param name="test" value="true"/> |
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249 </section> |
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250 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> |
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251 <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/> |
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252 <param name="out_type" value="mzML"/> |
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253 <param name="lossy_compression" value="true"/> |
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254 <param name="full_meta" value="true"/> |
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255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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256 <output name="ctd_out" ftype="xml"> |
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257 <assert_contents> |
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258 <is_valid_xml/> |
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259 </assert_contents> |
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260 </output> |
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261 </test> |
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262 <!-- TOPP_OpenSwathWorkflow_14_step2 --> |
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263 <test expect_num_outputs="2"> |
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264 <section name="adv_opts"> |
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265 <param name="lossy_mass_accuracy" value="0.0001"/> |
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266 <param name="process_lowmemory" value="false"/> |
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267 <param name="lowmem_batchsize" value="500"/> |
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268 <param name="force" value="false"/> |
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269 <param name="test" value="true"/> |
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270 </section> |
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271 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> |
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272 <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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273 <param name="out_type" value="mzML"/> |
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274 <param name="lossy_compression" value="false"/> |
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275 <param name="full_meta" value="false"/> |
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276 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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277 <output name="ctd_out" ftype="xml"> |
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278 <assert_contents> |
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279 <is_valid_xml/> |
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280 </assert_contents> |
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281 </output> |
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282 </test> |
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9
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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283 </tests> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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284 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. |
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0
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285 |
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286 |
|
13
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287 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help> |
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9
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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288 <expand macro="references"/> |
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0
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289 </tool> |