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1 <tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter">
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2 <description>
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3 Extract portions of peak lists.
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4 </description>
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2
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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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0
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'FileFilter' --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 #if $mz.specify
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16 mz=${mz.min}:${mz.max}
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17 #end if
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18 #if $rt.specify
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19 rt=${rt.min}:${rt.max}
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20 #end if
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21 #if $intensity.specify
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22 int=${intensity.min}:${intensity.max}
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23 #end if
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24 sn=${signal_to_noise}
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25 in=${in}
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26 in_type=mzML
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27 out=${out}
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28 out_type=mzML
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29 </configfile>
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30 </configfiles>
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31 <inputs>
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32 <param format="mzml" name="in" type="data" label="Input mzML File"/>
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33 <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" />
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34 <conditional name="mz">
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35 <param type="boolean" name="specify" label="Filter by m/z" />
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36 <when value="true">
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37 <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" />
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38 <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" />
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39 </when>
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40 </conditional>
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41 <conditional name="rt">
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42 <param type="boolean" name="specify" label="Filter by retention time" />
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43 <when value="true">
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44 <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" />
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45 <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" />
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46 </when>
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47 </conditional>
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48 <conditional name="intensity">
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49 <param type="boolean" name="specify" label="Filter by intensity" />
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50 <when value="true">
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51 <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" />
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52 <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" />
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data format="mzml" name="out" />
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58 </outputs>
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59 <help>
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60 **What it does**
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61
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62 Extracts portions of the data from an mzML.
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63
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64 **Citation**
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65
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66 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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67
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68 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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69 </help>
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70 </tool>
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