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comparison FileConverter.xml @ 0:2ef180905190 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:46:54 -0500
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children bb0bcfe80e24
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-1:000000000000 0:2ef180905190
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="FileConverter" name="FileConverter" version="2.1.0">
5 <description>Converts between different MS file formats.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FileConverter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FileConverter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_UID_postprocessing:
19 -UID_postprocessing $param_UID_postprocessing
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_out_type:
25 -out_type
26 #if " " in str($param_out_type):
27 "$param_out_type"
28 #else
29 $param_out_type
30 #end if
31 #end if
32 #if $param_write_mzML_index:
33 -write_mzML_index
34 #end if
35 #if $adv_opts.adv_opts_selector=='advanced':
36 #if $adv_opts.param_TIC_DTA2D:
37 -TIC_DTA2D
38 #end if
39 #if $adv_opts.param_MGF_compact:
40 -MGF_compact
41 #end if
42 #if $adv_opts.param_process_lowmemory:
43 -process_lowmemory
44 #end if
45 #if $adv_opts.param_force:
46 -force
47 #end if
48 #end if
49 </command>
50 <inputs>
51 <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
52 <param name="param_UID_postprocessing" display="radio" type="select" optional="False" 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">
53 <option value="none">none</option>
54 <option value="ensure" selected="true">ensure</option>
55 <option value="reassign">reassign</option>
56 </param>
57 <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) ">
58 <option value="mzData">mzData</option>
59 <option value="mzXML">mzXML</option>
60 <option value="mzML">mzML</option>
61 <option value="cachedMzML">cachedMzML</option>
62 <option value="dta2d">dta2d</option>
63 <option value="mgf">mgf</option>
64 <option value="featureXML">featureXML</option>
65 <option value="consensusXML">consensusXML</option>
66 <option value="edta">edta</option>
67 <option value="csv">csv</option>
68 </param>
69 <param name="param_write_mzML_index" display="radio" 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) "/>
70 <expand macro="advanced_options">
71 <param name="param_TIC_DTA2D" display="radio" 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) "/>
72 <param name="param_MGF_compact" display="radio" 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) "/>
73 <param name="param_process_lowmemory" display="radio" 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"/>
74 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
75 </expand>
76 </inputs>
77 <outputs>
78 <data name="param_out" metadata_source="param_in" auto_format="true"/>
79 </outputs>
80 <help>Converts between different MS file formats.
81
82
83 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
84 </tool>