Mercurial > repos > recetox > msmetaenhancer

annotate msmetaenhancer.xml @ 1:4c328e0e59ab draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:23:58 +0000
parents 053ce79ed564
children 4ae5b466a805
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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2 <description>annotate MS data</description>
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4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 <expand macro="creator"/>
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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11 </requirements>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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13 <command detect_errors="exit_code"><![CDATA[
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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14 sh ${msmetaenhancer_python_cli}
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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15 ]]> </command>
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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17 <configfiles>
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18 <configfile name="msmetaenhancer_python_cli">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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19 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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20 --input_file "$input_file" \
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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21 --output_file "$output_file" \
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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22 #if len($ordered_jobs) != 0:
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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23 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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24 #else:
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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25 #set ordered_jobs = ""
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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26 #end if
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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27 #if $jobs != 'None':
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28 #set random_jobs = str($jobs)
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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29 #else:
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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30 #set random_jobs = ""
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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31 #end if
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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32 #set all_jobs = str($ordered_jobs) + str($random_jobs)
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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33 --jobs "$all_jobs"
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34 </configfile>
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35 </configfiles>
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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37 <inputs>
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38 <param label="Input spectra dataset" name="input_file" type="data" format="msp" />
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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40 <repeat name="ordered_jobs" title="Ordered conversions">
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41 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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42 <expand macro="job_options" />
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43 </param>
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44 </repeat>
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45
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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46 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
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47 <expand macro="job_options" />
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48 </param>
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49 </inputs>
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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51 <outputs>
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52 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
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53 </outputs>
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54
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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55 <tests>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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56 <test>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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57 <param name="input_file" value="sample.msp" ftype="msp" />
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58 <output name="output_file" file="sample_out.msp" ftype="msp"/>
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59 </test>
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60 </tests>
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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62 <help>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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63 <![CDATA[
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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64 @HELP@
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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65 ]]>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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66 </help>
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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68 </tool>