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annotate FileMerger.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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4
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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="2.0.0">
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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 -threads \${GALAXY_SLOTS:-24}
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26 #if $param_rt_concat_gap:
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27 -rt_concat:gap $param_rt_concat_gap
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28 #end if
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29
4
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30 ##if $rep_param_rt_concat_trafo_out:
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31 ##-rt_concat:trafo_out
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32 ## #for token in $rep_param_rt_concat_trafo_out:
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33 ## #if &quot; &quot; in str(token):
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34 ## &quot;$token.param_rt_concat_trafo_out&quot;
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35 ## #else
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36 ## $token.param_rt_concat_trafo_out
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37 ## #end if
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38 ## #end for
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39 ###end if
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40
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41 #if $param_raw_rt_auto:
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42 -raw:rt_auto
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43 #end if
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44
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45 #if $rep_param_raw_rt_custom:
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46 -raw:rt_custom
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47 #for token in $rep_param_raw_rt_custom:
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48 #if &quot; &quot; in str(token):
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49 &quot;$token.param_raw_rt_custom&quot;
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50 #else
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51 $token.param_raw_rt_custom
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52 #end if
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53 #end for
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54 #end if
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55 #if $param_raw_rt_filename:
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56 -raw:rt_filename
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57 #end if
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58 #if $param_raw_ms_level:
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59 -raw:ms_level $param_raw_ms_level
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60 #end if
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61 #if $adv_opts.adv_opts_selector=='advanced':
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62 #if $adv_opts.param_force:
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63 -force
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64 #end if
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65 #end if
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66 </command>
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67 <inputs>
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68 <param format="xml,mzml,mzxml,traml,txt,consensusxml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
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69 <sanitizer>
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70 <valid initial="string.printable">
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71 <remove value="'"/>
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72 <remove value="&quot;"/>
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73 </valid>
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74 </sanitizer>
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75 </param>
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76 <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
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77 <param help="(-gap) RT concatenation is enabled if a value &gt; 0 is set" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" name="param_rt_concat_gap" type="float" value="0.0"/>
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78 <param checked="false" falsevalue="" help="(-rt_auto) " label="Assign retention times automatically (integers starting at 1)" name="param_raw_rt_auto" optional="True" truevalue="-raw:rt_auto" type="boolean"/>
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79 <repeat min="0" name="rep_param_raw_rt_custom" title="param_raw_rt_custom">
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80 <param help="(-rt_custom) The number of given retention times must be equal to the number of input files" label="List of custom retention times that are assigned to the files" name="param_raw_rt_custom" size="30" type="text" value="0">
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81 <sanitizer>
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82 <valid initial="string.printable">
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83 <remove value="'"/>
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84 <remove value="&quot;"/>
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85 </valid>
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86 </sanitizer>
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87 </param>
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88 </repeat>
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89 <param checked="false" falsevalue="" help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'" 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," name="param_raw_rt_filename" optional="True" truevalue="-raw:rt_filename" type="boolean"/>
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90 <param help="(-ms_level) This option is useful for DTA files which do not contain MS level information" label="If 1 or higher, this number is assigned to spectra as the MS level" name="param_raw_ms_level" type="integer" value="0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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91 <expand macro="advanced_options">
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92 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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93 </expand>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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94 </inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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95 <outputs>
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96 <data format="xml" name="param_out"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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97 <!--<data format="trafoxml" name="param_rt_concat_trafo_out"/>-->
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98 </outputs>
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99 <help>Merges several MS files into one file.
0
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100
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101
4
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102 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
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103 </tool>