Mercurial > repos > galaxyp > openms_fileconverter
diff FileConverter.xml @ 11:f2388622d581 draft
"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 |
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--- a/FileConverter.xml Fri May 17 10:11:48 2019 -0400 +++ b/FileConverter.xml Wed Sep 09 12:46:14 2020 +0000 @@ -1,113 +1,116 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [File Handling]--> -<tool id="FileConverter" name="FileConverter" version="2.3.0"> +<tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Converts between different MS file formats.</description> <macros> <token name="@EXECUTABLE@">FileConverter</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FileConverter + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${out_type}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_UID_postprocessing: - -UID_postprocessing - #if " " in str($adv_opts.param_UID_postprocessing): - "$adv_opts.param_UID_postprocessing" - #else - $adv_opts.param_UID_postprocessing - #end if -#end if - #if $adv_opts.param_out_type: - -out_type - #if " " in str($adv_opts.param_out_type): - "$adv_opts.param_out_type" - #else - $adv_opts.param_out_type - #end if -#end if - #if $adv_opts.param_TIC_DTA2D: - -TIC_DTA2D -#end if - #if $adv_opts.param_MGF_compact: - -MGF_compact -#end if - #if $adv_opts.param_force_MaxQuant_compatibility: - -force_MaxQuant_compatibility -#end if - #if $adv_opts.param_force_TPP_compatibility: - -force_TPP_compatibility -#end if - #if $adv_opts.param_write_scan_index: - -write_scan_index - #if " " in str($adv_opts.param_write_scan_index): - "$adv_opts.param_write_scan_index" - #else - $adv_opts.param_write_scan_index - #end if -#end if - #if $adv_opts.param_lossy_compression: - -lossy_compression -#end if - #if $adv_opts.param_lossy_mass_accuracy: - -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy -#end if - #if $adv_opts.param_process_lowmemory: - -process_lowmemory -#end if - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${out_type}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <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) "/> - <expand macro="advanced_options"> - <param name="param_UID_postprocessing" display="radio" type="select" optional="False" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) <br>'none' keeps current IDs even if invalid. <br>'ensure' keeps current IDs but reassigns invalid ones. <br>'reassign' assigns new unique IDs"> + <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)"/> + <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"> + <option value="consensusXML">consensusxml</option> + <option value="csv">csv</option> + <option value="dta2d">dta2d</option> + <option value="edta">edta</option> + <option value="featureXML">featurexml</option> + <option value="mgf">mgf</option> + <option value="mzData">mzdata</option> + <option value="mzML">mzml</option> + <option value="mzXML">mzxml</option> + <expand macro="list_string_san"/> + </param> + <expand macro="adv_opts_macro"> + <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"> <option value="none">none</option> <option value="ensure" selected="true">ensure</option> <option value="reassign">reassign</option> + <expand macro="list_string_san"/> </param> - <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) "> - <option value="mzData">mzData</option> - <option value="mzXML">mzXML</option> - <option value="mzML">mzML</option> - <option value="cachedMzML">cachedMzML</option> - <option value="dta2d">dta2d</option> - <option value="mgf">mgf</option> - <option value="featureXML">featureXML</option> - <option value="consensusXML">consensusXML</option> - <option value="edta">edta</option> - <option value="csv">csv</option> + <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 -> DTA2D conversions" help=""/> + <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=""/> + <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=""/> + <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=""/> + <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=""/> + <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=""> + <option value="none" selected="true">none</option> + <option value="multiple">multiple</option> + <option value="single">single</option> + <expand macro="list_string_san"/> </param> - <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 -> DTA2D conversions" help="(-TIC_DTA2D) "/> - <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) "/> - <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) "/> - <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) "/> - <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"> - <option value="true" selected="true">true</option> - <option value="false">false</option> + <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"/> + <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=""/> + <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)"/> + <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"/> + <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=""/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> </param> - <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) "/> - <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)"/> - <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) <br>Note: this flag will prevent conversion from spectra to chromatograms"/> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" metadata_source="param_in" auto_format="true"/> + <data name="out" label="${tool.name} on ${on_string}: out"> + <change_format> + <when input="out_type" value="consensusXML" format="consensusxml"/> + <when input="out_type" value="csv" format="csv"/> + <when input="out_type" value="dta2d" format="dta2d"/> + <when input="out_type" value="edta" format="edta"/> + <when input="out_type" value="featureXML" format="featurexml"/> + <when input="out_type" value="mgf" format="mgf"/> + <when input="out_type" value="mzData" format="mzdata"/> + <when input="out_type" value="mzML" format="mzml"/> + <when input="out_type" value="mzXML" format="mzxml"/> + </change_format> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Converts between different MS file formats. + <tests> + <expand macro="autotest_FileConverter"/> + <expand macro="manutest_FileConverter"/> + </tests> + <help><![CDATA[Converts between different MS file formats. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileConverter.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FileConverter.html]]></help> + <expand macro="references"/> </tool>