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annotate kronik.xml @ 0:d796e6613d19 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
author galaxyp
date Mon, 23 May 2016 11:12:40 -0400
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d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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1 <tool id="kronik" name="Kronik" version="2.02">
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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2 <description>processes Hardklör features to find peptides by chromatographic profiling</description>
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3 <requirements>
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4 <requirement type="package" version="2.02">kronik</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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8 </stdio>
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9 <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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10 <inputs>
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11 <param name="inputfile" type="data" format="hk" label="Hardklör isotope distributions" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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12 <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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13 <param name="d" type="integer" value="3" label="Match tolerance" help="Minimum consecutive scans peptide must be found in" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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14 <param name="g" type="integer" value="1" label="Gap tolerance" help="Maximum amount of scans a peptide can skip to be considered in results" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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15 <param name="m" type="integer" value="8000" label="Max mass (Da)" help="Maximum mass of peptide isotope distribution" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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16 <param name="n" type="integer" value="600" label="Min mass (Da)" help="Minimum mass of peptide isotope distribution" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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17 <param name="p" type="integer" value="10" label="Mass accuracy (ppm)" help="Peptides in adjacent scans must differ by less than this value to be called the same." />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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18 </inputs>
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19 <outputs>
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20 <data format="kr" name="output" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="inputfile" value="hardklor_result.hk"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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25 <output name="output" file="kronik_result.kr" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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26 </test>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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27 </tests>
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28 <help>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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29 Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Hardklör and Krönik were designed to rapidly identify peptide and protein features in high resolution spectra of complex mixtures. These algorithms were developed to meet the demands of modern mass spectrometers that are capable of generating large amounts of robust mass spectrometry data. Spectra containing tens to hundreds of overlapping ion signals are reduced to a relevant list of observed monoisotopic mass values, charge states, and signal intensity values when using Hardklör. These features are then filtered, validated, and summarized by using Krönik for the analysis of liquid chromatography mass spectrometry (LC-MS) data.
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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30 </help>
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31 <citations>
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32 <citation type="doi">10.1002/0471250953.bi1318s37</citation>
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33 </citations>
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34 </tool>