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comparison FileConverter.xml @ 11:f2388622d581 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:46:14 +0000
parents 1a186cc82c8d
children 62e19948b50f
comparison
equal deleted inserted replaced
10:5ad0b5bf1deb 11:f2388622d581
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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileConverter" name="FileConverter" version="2.3.0"> 4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FileConverter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $adv_opts.adv_opts_selector=='advanced': 24
22 #if $adv_opts.param_UID_postprocessing: 25 set -o pipefail &&
23 -UID_postprocessing 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if " " in str($adv_opts.param_UID_postprocessing): 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 "$adv_opts.param_UID_postprocessing" 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #else 29 -in
27 $adv_opts.param_UID_postprocessing 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #end if 32 'out/output.${out_type}'
30 #if $adv_opts.param_out_type: 33
31 -out_type 34 ## Postprocessing
32 #if " " in str($adv_opts.param_out_type): 35 && mv 'out/output.${out_type}' '$out'
33 "$adv_opts.param_out_type" 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #else 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 $adv_opts.param_out_type 38 #end if]]></command>
36 #end if 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 #if $adv_opts.param_TIC_DTA2D: 41 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 -TIC_DTA2D 42 </configfiles>
40 #end if
41 #if $adv_opts.param_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_force_TPP_compatibility:
48 -force_TPP_compatibility
49 #end if
50 #if $adv_opts.param_write_scan_index:
51 -write_scan_index
52 #if " " in str($adv_opts.param_write_scan_index):
53 "$adv_opts.param_write_scan_index"
54 #else
55 $adv_opts.param_write_scan_index
56 #end if
57 #end if
58 #if $adv_opts.param_lossy_compression:
59 -lossy_compression
60 #end if
61 #if $adv_opts.param_lossy_mass_accuracy:
62 -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy
63 #end if
64 #if $adv_opts.param_process_lowmemory:
65 -process_lowmemory
66 #end if
67 #if $adv_opts.param_force:
68 -force
69 #end if
70 #end if
71 ]]></command>
72 <inputs> 43 <inputs>
73 <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) "/> 44 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw data sets(s)"/>
74 <expand macro="advanced_options"> 45 <param name="out_type" argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
75 <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"> 46 <option value="consensusXML">consensusxml</option>
47 <option value="csv">csv</option>
48 <option value="dta2d">dta2d</option>
49 <option value="edta">edta</option>
50 <option value="featureXML">featurexml</option>
51 <option value="mgf">mgf</option>
52 <option value="mzData">mzdata</option>
53 <option value="mzML">mzml</option>
54 <option value="mzXML">mzxml</option>
55 <expand macro="list_string_san"/>
56 </param>
57 <expand macro="adv_opts_macro">
58 <param name="UID_postprocessing" argument="-UID_postprocessing" display="radio" type="select" optional="false" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
76 <option value="none">none</option> 59 <option value="none">none</option>
77 <option value="ensure" selected="true">ensure</option> 60 <option value="ensure" selected="true">ensure</option>
78 <option value="reassign">reassign</option> 61 <option value="reassign">reassign</option>
62 <expand macro="list_string_san"/>
79 </param> 63 </param>
80 <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) "> 64 <param name="TIC_DTA2D" argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/>
81 <option value="mzData">mzData</option> 65 <param name="MGF_compact" argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/>
82 <option value="mzXML">mzXML</option> 66 <param name="force_MaxQuant_compatibility" argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
83 <option value="mzML">mzML</option> 67 <param name="convert_to_chromatograms" argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
84 <option value="cachedMzML">cachedMzML</option> 68 <param name="force_TPP_compatibility" argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
85 <option value="dta2d">dta2d</option> 69 <param name="change_im_format" argument="-change_im_format" display="radio" type="select" optional="false" label="[mzML output only] How to store ion mobility scans (none: no change in format, multiple: store each frame as multiple scans, one per drift time value, single: store whole frame as single scan with IM values in a FloatDataArray" help="">
86 <option value="mgf">mgf</option> 70 <option value="none" selected="true">none</option>
87 <option value="featureXML">featureXML</option> 71 <option value="multiple">multiple</option>
88 <option value="consensusXML">consensusXML</option> 72 <option value="single">single</option>
89 <option value="edta">edta</option> 73 <expand macro="list_string_san"/>
90 <option value="csv">csv</option>
91 </param> 74 </param>
92 <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) "/> 75 <param name="write_scan_index" argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
93 <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) "/> 76 <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
94 <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) "/> 77 <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
95 <param name="param_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_compatibility) "/> 78 <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" 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="Note: this flag will prevent conversion from spectra to chromatograms"/>
96 <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"> 79 <param name="no_peak_picking" argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
97 <option value="true" selected="true">true</option> 80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
98 <option value="false">false</option> 81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
82 <expand macro="list_string_san"/>
99 </param> 83 </param>
100 <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) "/>
101 <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)"/>
102 <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"/>
103 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
104 </expand> 84 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param>
105 </inputs> 88 </inputs>
106 <outputs> 89 <outputs>
107 <data name="param_out" metadata_source="param_in" auto_format="true"/> 90 <data name="out" label="${tool.name} on ${on_string}: out">
91 <change_format>
92 <when input="out_type" value="consensusXML" format="consensusxml"/>
93 <when input="out_type" value="csv" format="csv"/>
94 <when input="out_type" value="dta2d" format="dta2d"/>
95 <when input="out_type" value="edta" format="edta"/>
96 <when input="out_type" value="featureXML" format="featurexml"/>
97 <when input="out_type" value="mgf" format="mgf"/>
98 <when input="out_type" value="mzData" format="mzdata"/>
99 <when input="out_type" value="mzML" format="mzml"/>
100 <when input="out_type" value="mzXML" format="mzxml"/>
101 </change_format>
102 </data>
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
105 </data>
108 </outputs> 106 </outputs>
109 <help>Converts between different MS file formats. 107 <tests>
108 <expand macro="autotest_FileConverter"/>
109 <expand macro="manutest_FileConverter"/>
110 </tests>
111 <help><![CDATA[Converts between different MS file formats.
110 112
111 113
112 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileConverter.html</help> 114 For more information, visit http://www.openms.de/documentation/TOPP_FileConverter.html]]></help>
115 <expand macro="references"/>
113 </tool> 116 </tool>