Mercurial > repos > galaxyp > openms_idscoreswitcher

annotate IDScoreSwitcher.xml @ 0:96484de4d4bd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:26:54 -0500
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96484de4d4bd 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: [Utilities]-->
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4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="2.1.0">
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5 <description>Switches between different scores of peptide or protein hits in identification data</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDScoreSwitcher</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>IDScoreSwitcher
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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 $param_new_score:
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22 -new_score "$param_new_score"
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23 #end if
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24 #if $param_new_score_orientation:
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25 -new_score_orientation
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26 #if " " in str($param_new_score_orientation):
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27 "$param_new_score_orientation"
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28 #else
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29 $param_new_score_orientation
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30 #end if
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31 #end if
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32 #if $param_new_score_type:
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33 -new_score_type "$param_new_score_type"
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34 #end if
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35 #if $param_old_score:
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36 -old_score "$param_old_score"
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37 #end if
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38 #if $param_proteins:
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39 -proteins
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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="idxml" optional="False" label="Input file" help="(-in) "/>
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49 <param name="param_new_score" type="text" size="30" label="Name of the meta value to use as the new score" help="(-new_score) ">
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50 <sanitizer>
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51 <valid initial="string.printable">
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52 <remove value="'"/>
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53 <remove value="&quot;"/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param name="param_new_score_orientation" display="radio" type="select" optional="False" label="Orientation of the new score (are higher or lower values better?)" help="(-new_score_orientation) ">
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58 <option value="lower_better">lower_better</option>
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59 <option value="higher_better">higher_better</option>
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60 </param>
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61 <param name="param_new_score_type" type="text" size="30" label="Name to use as the type of the new score (default: same as 'new_score')" help="(-new_score_type) ">
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62 <sanitizer>
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63 <valid initial="string.printable">
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64 <remove value="'"/>
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65 <remove value="&quot;"/>
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66 </valid>
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67 </sanitizer>
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68 </param>
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69 <param name="param_old_score" type="text" size="30" label="Name to use for the meta value storing the old score (default: old score type)" help="(-old_score) ">
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70 <sanitizer>
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71 <valid initial="string.printable">
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72 <remove value="'"/>
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73 <remove value="&quot;"/>
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74 </valid>
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75 </sanitizer>
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76 </param>
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77 <param name="param_proteins" display="radio" type="boolean" truevalue="-proteins" falsevalue="" checked="false" optional="True" label="Apply to protein scores instead of PSM scores" help="(-proteins) "/>
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78 <expand macro="advanced_options">
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79 <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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80 </expand>
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81 </inputs>
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82 <outputs>
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83 <data name="param_out" format="idxml"/>
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84 </outputs>
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85 <help>Switches between different scores of peptide or protein hits in identification data
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86
96484de4d4bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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96484de4d4bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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88 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDScoreSwitcher.html</help>
96484de4d4bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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89 </tool>