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comparison FileConverter.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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-1:000000000000 0:3d84209d3178
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="FileConverter" name="FileConverter" version="1.12.0">
3 <description>Converts between different MS file formats.</description>
4 <macros>
5 <token name="@EXECUTABLE@">FileConverter</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>FileConverter
11
12 -in ${param_in}
13 -in_type ${param_in_type}
14 -UID_postprocessing ${param_UID_postprocessing}
15 -out ${param_out}
16 -out_type ${param_out_type}
17 ${param_write_mzML_index}
18 -threads \${GALAXY_SLOTS:-24}
19 #if $adv_opts.adv_opts_selector=='advanced':
20 ${adv_opts.param_TIC_DTA2D}
21 ${adv_opts.param_MGF_compact}
22 ${adv_opts.param_process_lowmemory}
23 #end if
24 </command>
25 <inputs>
26 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/>
27 <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content#br#" help="(-in_type)">
28 <option value="mzData">mzData</option>
29 <option value="mzXML">mzXML</option>
30 <option value="mzML">mzML</option>
31 <option value="dta">dta</option>
32 <option value="dta2d">dta2d</option>
33 <option value="mgf">mgf</option>
34 <option value="featureXML">featureXML</option>
35 <option value="consensusXML">consensusXML</option>
36 <option value="ms2">ms2</option>
37 <option value="fid">fid</option>
38 <option value="tsv">tsv</option>
39 <option value="peplist">peplist</option>
40 <option value="kroenik">kroenik</option>
41 <option value="edta">edta</option>
42 </param>
43 <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data.#br#'none' keeps current IDs even if invalid.#br#'ensure' keeps current IDs but reassigns invalid ones.#br#'reassign' assigns new unique IDs." help="(-UID_postprocessing)">
44 <option value="none">none</option>
45 <option value="ensure">ensure</option>
46 <option value="reassign">reassign</option>
47 </param>
48 <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." help="(-out_type)">
49 <option value="mzData">mzData</option>
50 <option value="mzXML">mzXML</option>
51 <option value="mzML">mzML</option>
52 <option value="dta2d">dta2d</option>
53 <option value="mgf">mgf</option>
54 <option value="featureXML">featureXML</option>
55 <option value="consensusXML">consensusXML</option>
56 <option value="edta">edta</option>
57 <option value="csv">csv</option>
58 </param>
59 <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index true" falsevalue="-write_mzML_index false" checked="false" optional="True" label="Whether to add an index to the file when writing mzML files" help="(-write_mzML_index)"/>
60 <expand macro="advanced_options">
61 <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D true" falsevalue="-TIC_DTA2D false" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions." help="(-TIC_DTA2D)"/>
62 <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact true" falsevalue="-MGF_compact false" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact)"/>
63 <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory true" falsevalue="-process_lowmemory false" checked="false" optional="True" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." help="(-process_lowmemory)"/>
64 </expand>
65 </inputs>
66 <outputs>
67 <data name="param_out" label="Output file" format="tabular">
68 <change_format>
69 <when input="param_out_type" value="mzXML" format="mzXML"/>
70 <when input="param_out_type" value="mzML" format="mzML"/>
71 <when input="param_out_type" value="mgf" format="mgf"/>
72 <when input="param_out_type" value="featureXML" format="featureXML"/>
73 <when input="param_out_type" value="consensusXML" format="consensusXML"/>
74 </change_format>
75 </data>
76 </outputs>
77 <help>**What it does**
78
79 Converts between different MS file formats.
80
81
82 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html
83
84 @REFERENCES@
85 </help>
86 </tool>