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comparison FileConverter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="FileConverter" name="FileConverter" version="1.12.0"> 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 <description>Converts between different MS file formats.</description> 3 <!--Proposed Tool Section: [File Handling]-->
4 <macros> 4 <tool id="FileConverter" name="FileConverter" version="2.0.0">
5 <token name="@EXECUTABLE@">FileConverter</token> 5 <description>Converts between different MS file formats.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FileConverter</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FileConverter 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FileConverter
11 14
12 -in ${param_in} 15 #if $param_in:
13 -in_type ${param_in_type} 16 -in $param_in
14 -UID_postprocessing ${param_UID_postprocessing} 17 #end if
15 -out ${param_out} 18 #if $param_UID_postprocessing:
16 -out_type ${param_out_type} 19 -UID_postprocessing
17 ${param_write_mzML_index} 20 #if &quot; &quot; in str($param_UID_postprocessing):
18 -threads \${GALAXY_SLOTS:-24} 21 &quot;$param_UID_postprocessing&quot;
22 #else
23 $param_UID_postprocessing
24 #end if
25 #end if
26 #if $param_out:
27 -out $param_out
28 #end if
29 #if $param_out_type:
30 -out_type
31 #if &quot; &quot; in str($param_out_type):
32 &quot;$param_out_type&quot;
33 #else
34 $param_out_type
35 #end if
36 #end if
37 #if $param_write_mzML_index:
38 -write_mzML_index
39 #end if
40 -threads \${GALAXY_SLOTS:-24}
19 #if $adv_opts.adv_opts_selector=='advanced': 41 #if $adv_opts.adv_opts_selector=='advanced':
20 ${adv_opts.param_TIC_DTA2D} 42 #if $adv_opts.param_TIC_DTA2D:
21 ${adv_opts.param_MGF_compact} 43 -TIC_DTA2D
22 ${adv_opts.param_process_lowmemory} 44 #end if
45 #if $adv_opts.param_MGF_compact:
46 -MGF_compact
47 #end if
48 #if $adv_opts.param_process_lowmemory:
49 -process_lowmemory
50 #end if
51 #if $adv_opts.param_force:
52 -force
53 #end if
23 #end if 54 #end if
24 </command> 55 </command>
25 <inputs> 56 <inputs>
26 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/> 57 <param format="xml,mzml,mzxml,tabular,txt,consensusxml" help="(-in) " label="Input file to convert" name="param_in" optional="False" type="data"/>
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)"> 58 <param 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" label="unique ID post-processing for output data" name="param_UID_postprocessing" optional="True" type="select" value="ensure">
28 <option value="mzData">mzData</option> 59 <option value="none">none</option>
29 <option value="mzXML">mzXML</option> 60 <option value="ensure">ensure</option>
30 <option value="mzML">mzML</option> 61 <option value="reassign">reassign</option>
31 <option value="dta">dta</option> 62 </param>
32 <option value="dta2d">dta2d</option> 63 <param help="(-out_type) " label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" name="param_out_type" optional="True" type="select">
33 <option value="mgf">mgf</option> 64 <option value="mzData">mzData</option>
34 <option value="featureXML">featureXML</option> 65 <option value="mzXML">mzXML</option>
35 <option value="consensusXML">consensusXML</option> 66 <option value="mzML">mzML</option>
36 <option value="ms2">ms2</option> 67 <option value="dta2d">dta2d</option>
37 <option value="fid">fid</option> 68 <option value="mgf">mgf</option>
38 <option value="tsv">tsv</option> 69 <option value="featureXML">featureXML</option>
39 <option value="peplist">peplist</option> 70 <option value="consensusXML">consensusXML</option>
40 <option value="kroenik">kroenik</option> 71 <option value="edta">edta</option>
41 <option value="edta">edta</option> 72 <option value="csv">csv</option>
42 </param> 73 </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)"> 74 <param checked="false" falsevalue="" help="(-write_mzML_index) " label="Add an index to the file when writing mzML files (default: no index)" name="param_write_mzML_index" optional="True" truevalue="-write_mzML_index" type="boolean"/>
44 <option value="none">none</option> 75 <expand macro="advanced_options">
45 <option value="ensure">ensure</option> 76 <param checked="false" falsevalue="" help="(-TIC_DTA2D) " label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" name="param_TIC_DTA2D" optional="True" truevalue="-TIC_DTA2D" type="boolean"/>
46 <option value="reassign">reassign</option> 77 <param checked="false" falsevalue="" help="(-MGF_compact) " label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" name="param_MGF_compact" optional="True" truevalue="-MGF_compact" type="boolean"/>
47 </param> 78 <param checked="false" falsevalue="" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms" 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)" name="param_process_lowmemory" optional="True" truevalue="-process_lowmemory" type="boolean"/>
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)"> 79 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
49 <option value="mzData">mzData</option> 80 </expand>
50 <option value="mzXML">mzXML</option> 81 </inputs>
51 <option value="mzML">mzML</option> 82 <outputs>
52 <option value="dta2d">dta2d</option> 83 <data name="param_out" metadata_source="param_in" format="mgf">
53 <option value="mgf">mgf</option> 84 <change_format>
54 <option value="featureXML">featureXML</option> 85 <when input="param_out_type" value="mzData" format="mzData" />
55 <option value="consensusXML">consensusXML</option> 86 <when input="param_out_type" value="mzXML" format="mzXML" />
56 <option value="edta">edta</option> 87 <when input="param_out_type" value="mzML" format="mzML" />
57 <option value="csv">csv</option> 88 <when input="param_out_type" value="dta2d" format="dta2d" />
58 </param> 89 <when input="param_out_type" value="featureXML" format="featureXML" />
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)"/> 90 <when input="param_out_type" value="consensusXML" format="consensusXML" />
60 <expand macro="advanced_options"> 91 <when input="param_out_type" value="edta" format="edta" />
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)"/> 92 <when input="param_out_type" value="csv" format="csv" />
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)"/> 93 </change_format>
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> 94 </data>
76 </outputs> 95 </outputs>
77 <help>**What it does** 96 <help>Converts between different MS file formats.
78
79 Converts between different MS file formats.
80 97
81 98
82 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html 99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
83 100 </tool>
84 @REFERENCES@
85 </help>
86 </tool>