annotate id_file_converter.xml @ 3:8fa16707e162 draft

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author galaxyp
date Fri, 10 May 2013 17:31:59 -0400
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1 <tool id="openms_id_file_converter" version="0.1.0" name="ID File Converter">
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2 <description>
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3 Converts identification engine file formats.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio" />
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9 <expand macro="requires" />
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'IDFileConverter' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=${in}
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16 in_type=${in.ext}
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17 out=${out}
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18 out_type=${output_type}
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19 </configfile>
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20 </configfiles>
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21 <inputs>
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22 <param format="pepxml,protxml,idxml" name="in" type="data" label="Input Identification File"/>
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23 <param name="output_type" type="select" label="Output Type">
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24 <option value="idxml">idXML</option>
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25 <option value="pepxml">pepXM</option>
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26 <option value="mzid">mzIdentML</option>
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27 <option value="fasta">FASTA</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data format="idxml" name="out">
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32 <change_format>
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33 <when input="output_type" value="pepxml" format="pepxml" />
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34 <when input="output_type" value="mzid" format="mzid" />
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35 <when input="output_type" value="fasta" format="fasta" />
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36 </change_format>
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37 </data>
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38 </outputs>
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39 <help>
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40 **What it does**
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41
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42 Shows basic information about the file, such as data ranges and file type.
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43
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44 **Citation**
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45
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46 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
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48 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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49 </help>
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50 </tool>