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comparison FileConverter.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="FileConverter" name="FileConverter" version="2.0.0">
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 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_UID_postprocessing:
16 -UID_postprocessing
17 #if " " in str($param_UID_postprocessing):
18 "$param_UID_postprocessing"
19 #else
20 $param_UID_postprocessing
21 #end if
22 #end if
23 #if $param_out:
24 -out $param_out
25 #end if
26 #if $param_out_type:
27 -out_type
28 #if " " in str($param_out_type):
29 "$param_out_type"
30 #else
31 $param_out_type
32 #end if
33 #end if
34 #if $param_write_mzML_index:
35 -write_mzML_index
36 #end if
37 -threads \${GALAXY_SLOTS:-24}
38 #if $adv_opts.adv_opts_selector=='advanced':
39 #if $adv_opts.param_TIC_DTA2D:
40 -TIC_DTA2D
41 #end if
42 #if $adv_opts.param_MGF_compact:
43 -MGF_compact
44 #end if
45 #if $adv_opts.param_process_lowmemory:
46 -process_lowmemory
47 #end if
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #end if
52 </command>
53 <inputs>
54 <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
55 <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs">
56 <option value="none">none</option>
57 <option value="ensure">ensure</option>
58 <option value="reassign">reassign</option>
59 </param>
60 <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
61 <option value="mzData">mzData</option>
62 <option value="mzXML">mzXML</option>
63 <option value="mzML">mzML</option>
64 <option value="dta2d">dta2d</option>
65 <option value="mgf">mgf</option>
66 <option value="featureXML">featureXML</option>
67 <option value="consensusXML">consensusXML</option>
68 <option value="edta">edta</option>
69 <option value="csv">csv</option>
70 </param>
71 <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index" falsevalue="" checked="false" optional="True" label="Add an index to the file when writing mzML files (default: no index)" help="(-write_mzML_index) "/>
72 <expand macro="advanced_options">
73 <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/>
74 <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact" falsevalue="" 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) "/>
75 <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory" falsevalue="" 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)" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms"/>
76 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
77 </expand>
78 </inputs>
79 <outputs>
80 <data name="param_out" metadata_source="param_in" format="input"/>
81 </outputs>
82 <help>**What it does**
83
84 Converts between different MS file formats.
85
86
87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
88 <expand macro="references"/>
89 </tool>