Mercurial > repos > galaxyp > openms_openswathdecoygenerator
annotate OpenSwathDecoyGenerator.xml @ 13:496cf619e311 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 19:18:22 +0000 |
| parents | 3769d3a7e9ba |
| children |
| rev | line source |
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d38ef9cbc114
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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5
829f134aab22
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: [Targeted Experiments]--> |
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496cf619e311
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" 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>Generates decoys according to different models for a specific TraML</description> |
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d38ef9cbc114
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
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d38ef9cbc114
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> |
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d38ef9cbc114
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> |
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d38ef9cbc114
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
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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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d38ef9cbc114
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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1814187218fe
"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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1814187218fe
"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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"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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1814187218fe
"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($in.ext)' && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir out && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 ## Main program call |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 |
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1814187218fe
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 set -o pipefail && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 @EXECUTABLE@ -write_ctd ./ && |
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1814187218fe
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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1814187218fe
"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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"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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"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($in.ext)' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 -out |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 'out/output.${out_type}' |
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d38ef9cbc114
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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"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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"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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"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 $OPTIONAL_OUTPUTS |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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"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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"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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"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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"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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"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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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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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="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> |
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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=""> |
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44 <option value="TraML">traml</option> |
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45 <option value="pqp">pqp</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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46 <option value="tsv">tabular (tsv)</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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47 <expand macro="list_string_san" name="out_type"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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48 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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49 <param argument="-method" type="select" optional="true" label="Decoy generation method" help=""> |
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50 <option value="shuffle" selected="true">shuffle</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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51 <option value="pseudo-reverse">pseudo-reverse</option> |
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52 <option value="reverse">reverse</option> |
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53 <option value="shift">shift</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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54 <expand macro="list_string_san" name="method"/> |
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55 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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56 <param argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help=""> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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57 <expand macro="list_string_san" name="decoy_tag"/> |
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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 </param> |
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59 <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/> |
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60 <expand macro="adv_opts_macro"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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61 <param argument="-min_decoy_fraction" type="float" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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62 <param argument="-aim_decoy_fraction" type="float" optional="true" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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63 <param argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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64 <param argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/> |
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65 <param argument="-shift_precursor_mz_shift" type="float" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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66 <param argument="-shift_product_mz_shift" type="float" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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67 <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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68 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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69 <expand macro="list_string_san" name="allowed_fragment_types"/> |
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70 </param> |
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71 <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> |
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72 <expand macro="list_string_san" name="allowed_fragment_charges"/> |
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73 </param> |
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74 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/> |
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75 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/> |
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76 <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/> |
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77 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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78 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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79 <expand macro="list_string_san" name="test"/> |
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9
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80 </param> |
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81 </expand> |
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11
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82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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9
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83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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0
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84 </param> |
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85 </inputs> |
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86 <outputs> |
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13
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87 <data name="out" label="${tool.name} on ${on_string}: out" format="traml"> |
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88 <change_format> |
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89 <when input="out_type" value="pqp" format="pqp"/> |
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90 <when input="out_type" value="tsv" format="tabular"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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91 </change_format> |
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92 </data> |
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93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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95 </data> |
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0
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96 </outputs> |
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13
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97 <tests><!-- TOPP_OpenSwathDecoyGenerator_test_1 --> |
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98 <test expect_num_outputs="2"> |
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99 <section name="adv_opts"> |
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100 <param name="min_decoy_fraction" value="0.8"/> |
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101 <param name="aim_decoy_fraction" value="1.0"/> |
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102 <param name="shuffle_max_attempts" value="30"/> |
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103 <param name="shuffle_sequence_identity_threshold" value="0.5"/> |
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104 <param name="shift_precursor_mz_shift" value="0.0"/> |
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105 <param name="shift_product_mz_shift" value="20.0"/> |
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106 <param name="product_mz_threshold" value="0.025"/> |
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107 <param name="allowed_fragment_types" value="b,y"/> |
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108 <param name="allowed_fragment_charges" value="1,2,3,4"/> |
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109 <param name="enable_detection_specific_losses" value="false"/> |
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110 <param name="enable_detection_unspecific_losses" value="false"/> |
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111 <param name="separate" value="true"/> |
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112 <param name="force" value="false"/> |
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113 <param name="test" value="true"/> |
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114 </section> |
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115 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> |
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116 <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> |
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117 <param name="out_type" value="TraML"/> |
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118 <param name="method" value="pseudo-reverse"/> |
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119 <param name="decoy_tag" value="DECOY_"/> |
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120 <param name="switchKR" value="false"/> |
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121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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122 <output name="ctd_out" ftype="xml"> |
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123 <assert_contents> |
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124 <is_valid_xml/> |
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125 </assert_contents> |
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126 </output> |
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127 </test> |
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128 <!-- TOPP_OpenSwathDecoyGenerator_test_2 --> |
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129 <test expect_num_outputs="2"> |
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130 <section name="adv_opts"> |
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131 <param name="min_decoy_fraction" value="0.8"/> |
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132 <param name="aim_decoy_fraction" value="1.0"/> |
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133 <param name="shuffle_max_attempts" value="30"/> |
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134 <param name="shuffle_sequence_identity_threshold" value="0.5"/> |
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135 <param name="shift_precursor_mz_shift" value="0.0"/> |
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136 <param name="shift_product_mz_shift" value="20.0"/> |
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137 <param name="product_mz_threshold" value="0.8"/> |
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138 <param name="allowed_fragment_types" value="b,y"/> |
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139 <param name="allowed_fragment_charges" value="1,2,3,4"/> |
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140 <param name="enable_detection_specific_losses" value="false"/> |
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141 <param name="enable_detection_unspecific_losses" value="false"/> |
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142 <param name="separate" value="false"/> |
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143 <param name="force" value="false"/> |
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144 <param name="test" value="true"/> |
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145 </section> |
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146 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> |
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147 <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> |
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148 <param name="out_type" value="TraML"/> |
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149 <param name="method" value="pseudo-reverse"/> |
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150 <param name="decoy_tag" value="DECOY_"/> |
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151 <param name="switchKR" value="false"/> |
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152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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153 <output name="ctd_out" ftype="xml"> |
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154 <assert_contents> |
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155 <is_valid_xml/> |
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156 </assert_contents> |
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157 </output> |
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158 </test> |
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159 <!-- TOPP_OpenSwathDecoyGenerator_test_3 --> |
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160 <test expect_num_outputs="2"> |
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161 <section name="adv_opts"> |
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162 <param name="min_decoy_fraction" value="0.8"/> |
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163 <param name="aim_decoy_fraction" value="1.0"/> |
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164 <param name="shuffle_max_attempts" value="30"/> |
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165 <param name="shuffle_sequence_identity_threshold" value="0.5"/> |
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166 <param name="shift_precursor_mz_shift" value="0.0"/> |
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167 <param name="shift_product_mz_shift" value="20.0"/> |
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168 <param name="product_mz_threshold" value="0.025"/> |
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169 <param name="allowed_fragment_types" value="b,y"/> |
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170 <param name="allowed_fragment_charges" value="1,2,3,4"/> |
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171 <param name="enable_detection_specific_losses" value="false"/> |
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172 <param name="enable_detection_unspecific_losses" value="false"/> |
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173 <param name="separate" value="true"/> |
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174 <param name="force" value="false"/> |
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175 <param name="test" value="true"/> |
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176 </section> |
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177 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> |
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178 <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> |
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179 <param name="out_type" value="TraML"/> |
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180 <param name="method" value="pseudo-reverse"/> |
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181 <param name="decoy_tag" value="DECOY_"/> |
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182 <param name="switchKR" value="false"/> |
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183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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184 <output name="ctd_out" ftype="xml"> |
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185 <assert_contents> |
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186 <is_valid_xml/> |
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187 </assert_contents> |
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188 </output> |
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189 </test> |
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190 <!-- TOPP_OpenSwathDecoyGenerator_test_4 --> |
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191 <test expect_num_outputs="2"> |
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192 <section name="adv_opts"> |
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193 <param name="min_decoy_fraction" value="0.4"/> |
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194 <param name="aim_decoy_fraction" value="1.0"/> |
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195 <param name="shuffle_max_attempts" value="30"/> |
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196 <param name="shuffle_sequence_identity_threshold" value="0.5"/> |
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197 <param name="shift_precursor_mz_shift" value="0.0"/> |
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198 <param name="shift_product_mz_shift" value="20.0"/> |
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199 <param name="product_mz_threshold" value="0.025"/> |
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200 <param name="allowed_fragment_types" value="b,y"/> |
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201 <param name="allowed_fragment_charges" value="1,2,3,4"/> |
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202 <param name="enable_detection_specific_losses" value="true"/> |
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203 <param name="enable_detection_unspecific_losses" value="true"/> |
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204 <param name="separate" value="true"/> |
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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="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> |
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209 <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> |
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210 <param name="out_type" value="TraML"/> |
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211 <param name="method" value="pseudo-reverse"/> |
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212 <param name="decoy_tag" value="DECOY_"/> |
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213 <param name="switchKR" value="true"/> |
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214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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215 <output name="ctd_out" ftype="xml"> |
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216 <assert_contents> |
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217 <is_valid_xml/> |
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218 </assert_contents> |
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219 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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220 </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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221 </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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222 <help><![CDATA[Generates decoys according to different models for a specific TraML |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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223 |
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224 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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225 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help> |
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226 <expand macro="references"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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227 </tool> |