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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0"
author galaxyp
date Wed, 26 May 2021 16:10:35 +0000
parents e8d7b7dc55fc
children
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e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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1 <tool id="metamorpheus_search" name="MetaMorpeus Database Search" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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2 <description>identify peptides by their fragmentation spectra</description>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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3 <macros>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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4 <import>macros.xml</import>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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5 </macros>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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6 <expand macro="requirements" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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7 <command detect_errors="exit_code"><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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8 @PREPARE_INPUTS@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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9 @LN_CALIB_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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10 @MERGE_TOMLS@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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11 metamorpheus
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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12 -t tasksettings.toml
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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13 -s ${inputs_dir}
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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14 -d #echo ' '.join($database_names)#
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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15 -o output
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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16 --mmsettings data
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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17 ]]></command>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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18 <configfiles>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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19 <configfile name="default_toml"><![CDATA[#slurp
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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20 @DEFAULT_SEARCH_TOML@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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21 ]]></configfile>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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22 <configfile name="user_toml">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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23 @SEARCH_CONFIG@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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24 @COMMON_CONFIG@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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25 </configfile>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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26 <configfile name="task_settings_toml">#slurp
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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27 </configfile>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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28 </configfiles>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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29 <inputs>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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30 <expand macro="input_spectrums" multiple="true" filetype="Calibrated Spectrum"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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31 <expand macro="calib_toml"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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32 <expand macro="input_databases"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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33 <expand macro="input_toml"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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34 <expand macro="common_params"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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35 <expand macro="search_params"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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36 </inputs>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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37 <outputs>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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38 <expand macro="output_settings_toml"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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39 <data name="results" format="txt" label="${tool.name} on ${on_string} results.txt" from_work_dir="output/allresults.txt"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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40 <data name="prose" format="txt" label="${tool.name} on ${on_string} prose.txt" from_work_dir="output/Task*SearchTask/prose.txt"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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41 <data name="allpsms" format="tabular" label="${tool.name} on ${on_string} AllPSMs.psmtsv" from_work_dir="output/Task*SearchTask/AllPSMs.psmtsv"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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42 <data name="allpsms_percolator" format="tabular" label="${tool.name} on ${on_string} AllPSMs_FormattedForPercolator.tab" from_work_dir="output/Task*SearchTask/AllPSMs_FormattedForPercolator.tab"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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43 <data name="allpeptides" format="tabular" label="${tool.name} on ${on_string} AllPeptides.psmtsv" from_work_dir="output/Task*SearchTask/AllPeptides.psmtsv"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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44 <data name="allquantifiedpeaks" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedPeaks.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedPeaks.tsv">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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45 </data>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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46 <data name="allquantifiedpeptides" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedPeptides.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedPeptides.tsv">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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47 </data>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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48 <data name="allquantifiedprotein" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedProteinGroups.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedProteinGroups.tsv">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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49 </data>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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50 <expand macro="search_collection_outputs"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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51 </outputs>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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52 <tests>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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53 <test>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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54 <param name="spectrums" ftype="mzml" value="SmallCalibratible_Yeast-calib.mzML"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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55 <param name="calib_tomls" ftype="toml" value="SmallCalibratible_Yeast-calib.toml"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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56 <param name="databases" ftype="fasta" value="SmallYeastGPTMD.xml"/>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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57 <output name="results">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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58 <assert_contents>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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59 <has_text text="Engine type: ProteinScoringAndFdrEngine" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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60 </assert_contents>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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61 </output>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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62 <output name="allpsms">
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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63 <assert_contents>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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64 <has_text text="KGNNTANATN[Common Artifact:Deamidation on N]SANTVQK" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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65 </assert_contents>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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66 </output>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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67 </test>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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68 </tests>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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69 <help><![CDATA[
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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70 @METAMORPHEUS_HELP@
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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71 ]]></help>
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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72 <expand macro="citations" />
e8d7b7dc55fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
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73 </tool>