Mercurial > repos > galaxyp > openms_filemerger
comparison FileMerger.xml @ 0:110f7ab62e67 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 10:00:11 -0500 |
| parents | |
| children | 397811d89637 |
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| -1:000000000000 | 0:110f7ab62e67 |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [File Handling]--> | |
| 4 <tool id="FileMerger" name="FileMerger" version="2.1.0"> | |
| 5 <description>Merges several MS files into one file.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">FileMerger</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>FileMerger | |
| 14 | |
| 15 -in | |
| 16 #for token in $param_in: | |
| 17 $token | |
| 18 #end for | |
| 19 #if $param_out: | |
| 20 -out $param_out | |
| 21 #end if | |
| 22 #if $param_annotate_file_origin: | |
| 23 -annotate_file_origin | |
| 24 #end if | |
| 25 #if $param_rt_concat_gap: | |
| 26 -rt_concat:gap $param_rt_concat_gap | |
| 27 #end if | |
| 28 | |
| 29 #if $rep_param_rt_concat_trafo_out: | |
| 30 -rt_concat:trafo_out | |
| 31 #for token in $rep_param_rt_concat_trafo_out: | |
| 32 #if " " in str(token): | |
| 33 "$token.param_rt_concat_trafo_out" | |
| 34 #else | |
| 35 $token.param_rt_concat_trafo_out | |
| 36 #end if | |
| 37 #end for | |
| 38 #end if | |
| 39 #if $param_raw_rt_auto: | |
| 40 -raw:rt_auto | |
| 41 #end if | |
| 42 | |
| 43 #if $rep_param_raw_rt_custom: | |
| 44 -raw:rt_custom | |
| 45 #for token in $rep_param_raw_rt_custom: | |
| 46 #if " " in str(token): | |
| 47 "$token.param_raw_rt_custom" | |
| 48 #else | |
| 49 $token.param_raw_rt_custom | |
| 50 #end if | |
| 51 #end for | |
| 52 #end if | |
| 53 #if $param_raw_rt_filename: | |
| 54 -raw:rt_filename | |
| 55 #end if | |
| 56 #if $param_raw_ms_level: | |
| 57 -raw:ms_level $param_raw_ms_level | |
| 58 #end if | |
| 59 #if $adv_opts.adv_opts_selector=='advanced': | |
| 60 #if $adv_opts.param_force: | |
| 61 -force | |
| 62 #end if | |
| 63 #end if | |
| 64 </command> | |
| 65 <inputs> | |
| 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) "> | |
| 67 <sanitizer> | |
| 68 <valid initial="string.printable"> | |
| 69 <remove value="'"/> | |
| 70 <remove value="""/> | |
| 71 </valid> | |
| 72 </sanitizer> | |
| 73 </param> | |
| 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 "file_origin" (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/> | |
| 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 > 0 is set"/> | |
| 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) "/> | |
| 77 <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom"> | |
| 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"> | |
| 79 <sanitizer> | |
| 80 <valid initial="string.printable"> | |
| 81 <remove value="'"/> | |
| 82 <remove value="""/> | |
| 83 </valid> | |
| 84 </sanitizer> | |
| 85 </param> | |
| 86 </repeat> | |
| 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'"/> | |
| 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"/> | |
| 89 <expand macro="advanced_options"> | |
| 90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 91 </expand> | |
| 92 </inputs> | |
| 93 <outputs> | |
| 94 <data name="param_out" format="featurexml"/> | |
| 95 <data name="param_rt_concat_trafo_out" format="trafoxml"/> | |
| 96 </outputs> | |
| 97 <help>Merges several MS files into one file. | |
| 98 | |
| 99 | |
| 100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help> | |
| 101 </tool> |