Mercurial > repos > galaxyp > openms_fileconverter

comparison FileConverter.xml @ 3:ed6890cfc90a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:42:16 -0400
parents bb0bcfe80e24
children 1fe84d73c19c
comparison
equal deleted inserted replaced
2:6634cad7d797 3:ed6890cfc90a
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileConverter" name="FileConverter" version="2.1.0"> 4 <tool id="FileConverter" name="FileConverter" version="2.2.0">
5 <description>Converts between different MS file formats.</description> 5 <description>Converts between different MS file formats.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileConverter</token> 7 <token name="@EXECUTABLE@">FileConverter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
13 <command>FileConverter 13 <command>FileConverter
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_UID_postprocessing:
19 -UID_postprocessing
20 #if " " in str($param_UID_postprocessing):
21 "$param_UID_postprocessing"
22 #else
23 $param_UID_postprocessing
24 #end if
25 #end if
26 #if $param_out: 18 #if $param_out:
27 -out $param_out 19 -out $param_out
28 #end if 20 #end if
29 #if $param_out_type: 21 #if $adv_opts.adv_opts_selector=='advanced':
30 -out_type 22 #if $adv_opts.param_UID_postprocessing:
31 #if " " in str($param_out_type): 23 -UID_postprocessing
32 "$param_out_type" 24 #if " " in str($adv_opts.param_UID_postprocessing):
25 "$adv_opts.param_UID_postprocessing"
33 #else 26 #else
34 $param_out_type 27 $adv_opts.param_UID_postprocessing
35 #end if 28 #end if
36 #end if 29 #end if
37 #if $param_write_mzML_index: 30 #if $adv_opts.param_out_type:
38 -write_mzML_index 31 -out_type
32 #if " " in str($adv_opts.param_out_type):
33 "$adv_opts.param_out_type"
34 #else
35 $adv_opts.param_out_type
36 #end if
39 #end if 37 #end if
40 #if $adv_opts.adv_opts_selector=='advanced':
41 #if $adv_opts.param_TIC_DTA2D: 38 #if $adv_opts.param_TIC_DTA2D:
42 -TIC_DTA2D 39 -TIC_DTA2D
43 #end if 40 #end if
44 #if $adv_opts.param_MGF_compact: 41 #if $adv_opts.param_MGF_compact:
45 -MGF_compact 42 -MGF_compact
43 #end if
44 #if $adv_opts.param_force_MaxQuant_compatibility:
45 -force_MaxQuant_compatibility
46 #end if
47 #if $adv_opts.param_write_scan_index:
48 -write_scan_index
49 #if " " in str($adv_opts.param_write_scan_index):
50 "$adv_opts.param_write_scan_index"
51 #else
52 $adv_opts.param_write_scan_index
53 #end if
54 #end if
55 #if $adv_opts.param_lossy_compression:
56 -lossy_compression
57 #end if
58 #if $adv_opts.param_lossy_mass_accuracy:
59 -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy
46 #end if 60 #end if
47 #if $adv_opts.param_process_lowmemory: 61 #if $adv_opts.param_process_lowmemory:
48 -process_lowmemory 62 -process_lowmemory
49 #end if 63 #end if
50 #if $adv_opts.param_force: 64 #if $adv_opts.param_force:
51 -force 65 -force
52 #end if 66 #end if
53 #end if 67 #end if
54 </command> 68 </command>
55 <inputs> 69 <inputs>
56 <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/> 70 <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
57 <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">
58 <option value="none">none</option>
59 <option value="ensure" selected="true">ensure</option>
60 <option value="reassign">reassign</option>
61 </param>
62 <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) ">
63 <option value="mzData">mzData</option>
64 <option value="mzXML">mzXML</option>
65 <option value="mzML">mzML</option>
66 <option value="cachedMzML">cachedMzML</option>
67 <option value="dta2d">dta2d</option>
68 <option value="mgf">mgf</option>
69 <option value="featureXML">featureXML</option>
70 <option value="consensusXML">consensusXML</option>
71 <option value="edta">edta</option>
72 <option value="csv">csv</option>
73 </param>
74 <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) "/>
75 <expand macro="advanced_options"> 71 <expand macro="advanced_options">
72 <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">
73 <option value="none">none</option>
74 <option value="ensure" selected="true">ensure</option>
75 <option value="reassign">reassign</option>
76 </param>
77 <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) ">
78 <option value="mzData">mzData</option>
79 <option value="mzXML">mzXML</option>
80 <option value="mzML">mzML</option>
81 <option value="cachedMzML">cachedMzML</option>
82 <option value="dta2d">dta2d</option>
83 <option value="mgf">mgf</option>
84 <option value="featureXML">featureXML</option>
85 <option value="consensusXML">consensusXML</option>
86 <option value="edta">edta</option>
87 <option value="csv">csv</option>
88 </param>
76 <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) "/> 89 <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) "/>
77 <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) "/> 90 <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) "/>
91 <param name="param_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
92 <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
93 <option value="true" selected="true">true</option>
94 <option value="false">false</option>
95 </param>
96 <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/>
97 <param name="param_lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression (" help="(-lossy_mass_accuracy) e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
78 <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"/> 98 <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"/>
79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 99 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
80 </expand> 100 </expand>
81 </inputs> 101 </inputs>
82 <outputs> 102 <outputs>