Mercurial > repos > galaxyp > openms_filemerger

annotate FileMerger.xml @ 2:39e8fde08881 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
author galaxyp
date Thu, 27 Apr 2017 13:22:07 -0400
parents 47d7f9fd5077
children 1dc8550349dd
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47d7f9fd5077 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: [File Handling]-->
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4 <tool id="FileMerger" name="FileMerger" version="2.1.0">
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5 <description>Merges several MS files into one file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileMerger</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>FileMerger
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_annotate_file_origin:
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23 -annotate_file_origin
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24 #end if
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25 #if $param_rt_concat_gap:
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26 -rt_concat:gap $param_rt_concat_gap
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27 #end if
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28
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29 #if $rep_param_rt_concat_trafo_out:
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30 -rt_concat:trafo_out
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31 #for token in $rep_param_rt_concat_trafo_out:
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32 #if " " in str(token):
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33 "$token.param_rt_concat_trafo_out"
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34 #else
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35 $token.param_rt_concat_trafo_out
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36 #end if
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37 #end for
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38 #end if
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39 #if $param_raw_rt_auto:
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40 -raw:rt_auto
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41 #end if
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42
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43 #if $rep_param_raw_rt_custom:
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44 -raw:rt_custom
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45 #for token in $rep_param_raw_rt_custom:
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46 #if " " in str(token):
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47 "$token.param_raw_rt_custom"
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48 #else
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49 $token.param_raw_rt_custom
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50 #end if
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51 #end for
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52 #end if
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53 #if $param_raw_rt_filename:
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54 -raw:rt_filename
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55 #end if
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56 #if $param_raw_ms_level:
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57 -raw:ms_level $param_raw_ms_level
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58 #end if
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59 #if $adv_opts.adv_opts_selector=='advanced':
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60 #if $adv_opts.param_force:
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61 -force
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62 #end if
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63 #end if
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64 </command>
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65 <inputs>
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66 <param name="param_in" type="data" format="mgf,mzml,mzxml,traml,featurexml,consensusxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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67 <sanitizer>
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68 <valid initial="string.printable">
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69 <remove value="'"/>
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70 <remove value="&quot;"/>
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71 </valid>
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72 </sanitizer>
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73 </param>
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74 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/>
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75 <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
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76 <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
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77 <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom">
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78 <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
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79 <sanitizer>
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80 <valid initial="string.printable">
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81 <remove value="'"/>
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82 <remove value="&quot;"/>
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83 </valid>
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84 </sanitizer>
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85 </param>
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86 </repeat>
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87 <param name="param_raw_rt_filename" display="radio" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'"/>
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88 <param name="param_raw_ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="(-ms_level) This option is useful for DTA files which do not contain MS level information"/>
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89 <expand macro="advanced_options">
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90 <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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91 </expand>
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92 </inputs>
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93 <outputs>
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94 <data name="param_out" format="featurexml"/>
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95 <data name="param_rt_concat_trafo_out" format="trafoxml"/>
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96 </outputs>
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97 <help>Merges several MS files into one file.
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98
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99
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100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
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101 </tool>