Mercurial > repos > galaxyp > openms_sequencecoveragecalculator

annotate SequenceCoverageCalculator.xml @ 11:5adf97f241ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:42:18 -0400
parents 3a7000f26f98
children 31779bcc3991
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9584ba614768 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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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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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0+galaxy1">
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5 <description>Prints information about idXML files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator
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13 #if $param_in_database:
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14 -in_database '$param_in_database'
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15 #end if
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16 #if $param_in_peptides:
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17 -in_peptides '$param_in_peptides'
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18 #end if
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19 #if $adv_opts.adv_opts_selector=='advanced':
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20 #if $adv_opts.param_force:
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21 -force
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22 #end if
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23 #end if
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25 ## fix output (https://github.com/OpenMS/OpenMS/issues/3605)
5adf97f241ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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26 ## - add header
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27 ## - remove reformat data
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28 ## - remove summary info
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29 ## - print summary info to stdout
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30 | sed '1i#protein\tcoverage%\t#unique hits'
5adf97f241ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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31 | sed 's/^\(.*\)(coverage%, #unique hits): \([0-9.]\+\)%, \([0-9]\+\)/\1\t\2\t\3/'
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32 | tee tmpout
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33 | egrep -v "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" > '$param_out'
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34 ##
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35 && cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took"
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36 ]]></command>
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37 <inputs>
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38 <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database) "/>
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39 <param name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/>
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40 <expand macro="advanced_options">
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41 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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42 </expand>
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43 </inputs>
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44 <outputs>
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45 <data name="param_out" format="tabular"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="param_in_database" ftype="fasta" value="OpenPepXL_input.fasta"/>
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50 <!-- generated with: IDFilter -best:strict -in ~/projects/OpenMS/src/tests/topp/OpenPepXL_output.idXML -out SequenceCoverageCalculator.idXML-->
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51 <param name="param_in_peptides" ftype="idxml" value="SequenceCoverageCalculator.idXML" />
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52 <output name="param_out" file="SequenceCoverageCalculator.tsv" ftype="tabular" />
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53 </test>
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54 </tests>
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55 <help>Prints information about idXML files.
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57
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58 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help>
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59 <expand macro="references"/>
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60 </tool>