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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FileInfo" name="FileInfo" version="1.12.0">
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3 <description>Shows basic information about the file, such as data ranges and file type.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FileInfo</token>
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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="requirements"/>
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10 <command>FileInfo
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11
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12 -in ${param_in}
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13 -in_type ${param_in_type}
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14 -out ${param_out}
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15 ${param_m}
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16 ${param_p}
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17 ${param_s}
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18 ${param_d}
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19 ${param_c}
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20 ${param_v}
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21 ${param_i}
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22 -threads \${GALAXY_SLOTS:-24}
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23 #if $adv_opts.adv_opts_selector=='advanced':
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24 -out_tsv ${adv_opts.param_out_tsv}
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25 #end if
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26 </command>
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27 <inputs>
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28 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML,idXML,pepXML" optional="False" label="input file " help="(-in)"/>
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29 <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-in_type)">
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30 <option value="mzData">mzData</option>
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31 <option value="mzXML">mzXML</option>
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32 <option value="mzML">mzML</option>
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33 <option value="dta">dta</option>
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34 <option value="dta2d">dta2d</option>
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35 <option value="mgf">mgf</option>
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36 <option value="featureXML">featureXML</option>
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37 <option value="consensusXML">consensusXML</option>
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38 <option value="idXML">idXML</option>
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39 <option value="pepXML">pepXML</option>
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40 <option value="fid">fid</option>
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41 </param>
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42 <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/>
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43 <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/>
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44 <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s)"/>
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45 <param name="param_d" type="boolean" truevalue="-d true" falsevalue="-d false" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d)"/>
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46 <param name="param_c" type="boolean" truevalue="-c true" falsevalue="-c false" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c)"/>
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47 <param name="param_v" type="boolean" truevalue="-v true" falsevalue="-v false" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v)"/>
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48 <param name="param_i" type="boolean" truevalue="-i true" falsevalue="-i false" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i)"/>
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49 </inputs>
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50 <outputs>
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51 <data name="param_out" label="Optional output file. If left out, the output is written to the command line." format="txt"/>
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52 <data name="param_out_tsv" label="Second optional output file. Tab separated flat text file." format="tabular"/>
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53 </outputs>
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54 <help>**What it does**
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55
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56 Shows basic information about the file, such as data ranges and file type.
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57
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58
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59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html
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60
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61 @REFERENCES@
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62 </help>
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63 </tool>
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