Mercurial > repos > galaxyp > pyprophet_merge

annotate pyprophet_merge.xml @ 0:73736112135d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
author galaxyp
date Wed, 26 Feb 2020 04:16:39 -0500
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73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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1 <tool id="pyprophet_merge" name="PyProphet merge" version="@VERSION@.0">
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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2 <description>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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3 Merge multiple osw files
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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4 </description>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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5 <macros>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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6 <import>macros.xml</import>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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7 </macros>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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8 <expand macro="requirements"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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9 <command detect_errors="aggressive">
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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10 <![CDATA[
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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11 pyprophet merge
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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12 --template='$template'
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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13 $same_run
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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14 --out='./output.osw'
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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15
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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16 #echo ' '.join(["'%s'" % $input for $input in $inputs])#
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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17 ]]>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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18 </command>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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19 <inputs>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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20 <param name="inputs" type="data" format="osw" multiple="true" label="Input file" help="This file needs to be in OSW format, an SQLite variant." />
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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21 <param argument="--template" type="data" format="sqlite" label="Template osw file" />
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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22 <param name="same_run" type="boolean" truevalue="--same_run" falsevalue="--no-same_run"
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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23 label="Input files are from same run (deletes run information)" help="(--same_run/--no-same_run)"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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24 </inputs>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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25 <outputs>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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26 <data name="output" format="osw" label="${tool.name} on ${on_string}: merged.osw" from_work_dir="output.osw" />
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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27 </outputs>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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28 <tests>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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29 <test>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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30 <param name="inputs" value="open_swath_output1.osw,open_swath_output2.osw" ftype="osw"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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31 <param name="template_file" ftype="pqp" value="patient_specific_OSW_optimized_decoys.pqp"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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32 <param name="same_run" value="False"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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33 <output name="output" file="merged.osw" compare="sim_size" />
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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34 </test>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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35 </tests>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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36 <help>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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37 <![CDATA[
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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38 **What it does**
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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39
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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40 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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41
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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42 Merge function of PyProphet: Takes several osw input files and merges them. For large experiments, it is recommended to subsample first.
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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43
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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44 PyProphet is a Python re-implementation of the mProphet algorithm (Reiter 2010 Nature Methods) optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in (Telemann 2014 Bioinformatics) and has since been extended to support new data types and analysis modes (Rosenberger 2017, Nature biotechnology and Nature methods).
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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45
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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46 For more information, visit @link@
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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47
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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48 ]]>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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49 </help>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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50 <expand macro="citations"/>
73736112135d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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51 </tool>