Mercurial > repos > galaxyp > openms_externalcalibration

annotate ExternalCalibration.xml @ 1:48ac6490c919 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 16:02:42 -0400
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children 5f51089db166
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b9ecf8eba490 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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="ExternalCalibration" name="ExternalCalibration" version="2.1.0">
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5 <description>Applies an external mass recalibration.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ExternalCalibration</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>ExternalCalibration
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_offset:
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22 -offset $param_offset
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23 #end if
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24 #if $param_slope:
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25 -slope $param_slope
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26 #end if
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27 #if $param_power:
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28 -power $param_power
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29 #end if
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30
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31 #if $rep_param_ms_level:
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32 -ms_level
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33 #for token in $rep_param_ms_level:
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34 #if " " in str(token):
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35 "$token.param_ms_level"
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36 #else
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37 $token.param_ms_level
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38 #end if
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39 #end for
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40 #end if
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41 #if $adv_opts.adv_opts_selector=='advanced':
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42 #if $adv_opts.param_force:
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43 -force
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44 #end if
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45 #end if
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46 </command>
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47 <inputs>
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48 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
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49 <param name="param_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/>
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50 <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/>
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51 <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/>
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52 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
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53 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Scans with other levels remain unchanged">
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54 <sanitizer>
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55 <valid initial="string.printable">
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56 <remove value="'"/>
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57 <remove value="&quot;"/>
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58 </valid>
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59 </sanitizer>
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60 </param>
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61 </repeat>
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62 <expand macro="advanced_options">
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63 <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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64 </expand>
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65 </inputs>
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66 <outputs>
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67 <data name="param_out" format="mzml"/>
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68 </outputs>
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69 <help>Applies an external mass recalibration.
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70
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71
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72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ExternalCalibration.html</help>
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73 </tool>