Mercurial > repos > bgruening > openms
diff FileConverter.xml @ 4:6ead64a594bd draft default tip
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 |
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--- a/FileConverter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileConverter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,86 +1,100 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="FileConverter" name="FileConverter" version="1.12.0"> - <description>Converts between different MS file formats.</description> - <macros> - <token name="@EXECUTABLE@">FileConverter</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>FileConverter +<?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 CTD2Galaxy.--> + <!--Proposed Tool Section: [File Handling]--> + <tool id="FileConverter" name="FileConverter" version="2.0.0"> + <description>Converts between different MS file formats.</description> + <macros> + <token name="@EXECUTABLE@">FileConverter</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FileConverter --in ${param_in} --in_type ${param_in_type} --UID_postprocessing ${param_UID_postprocessing} --out ${param_out} --out_type ${param_out_type} -${param_write_mzML_index} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_UID_postprocessing: + -UID_postprocessing + #if " " in str($param_UID_postprocessing): + "$param_UID_postprocessing" + #else + $param_UID_postprocessing + #end if +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_write_mzML_index: + -write_mzML_index +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_TIC_DTA2D} - ${adv_opts.param_MGF_compact} - ${adv_opts.param_process_lowmemory} + #if $adv_opts.param_TIC_DTA2D: + -TIC_DTA2D +#end if + #if $adv_opts.param_MGF_compact: + -MGF_compact +#end if + #if $adv_opts.param_process_lowmemory: + -process_lowmemory +#end if + #if $adv_opts.param_force: + -force +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/> - <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content#br#" help="(-in_type)"> - <option value="mzData">mzData</option> - <option value="mzXML">mzXML</option> - <option value="mzML">mzML</option> - <option value="dta">dta</option> - <option value="dta2d">dta2d</option> - <option value="mgf">mgf</option> - <option value="featureXML">featureXML</option> - <option value="consensusXML">consensusXML</option> - <option value="ms2">ms2</option> - <option value="fid">fid</option> - <option value="tsv">tsv</option> - <option value="peplist">peplist</option> - <option value="kroenik">kroenik</option> - <option value="edta">edta</option> - </param> - <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)"> - <option value="none">none</option> - <option value="ensure">ensure</option> - <option value="reassign">reassign</option> - </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="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> - <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)"/> - <expand macro="advanced_options"> - <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 -> DTA2D conversions." help="(-TIC_DTA2D)"/> - <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)"/> - <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)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="Output file" format="tabular"> - <change_format> - <when input="param_out_type" value="mzXML" format="mzXML"/> - <when input="param_out_type" value="mzML" format="mzML"/> - <when input="param_out_type" value="mgf" format="mgf"/> - <when input="param_out_type" value="featureXML" format="featureXML"/> - <when input="param_out_type" value="consensusXML" format="consensusXML"/> - </change_format> + <inputs> + <param format="xml,mzml,mzxml,tabular,txt,consensusxml" help="(-in) " label="Input file to convert" name="param_in" optional="False" type="data"/> + <param 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" label="unique ID post-processing for output data" name="param_UID_postprocessing" optional="True" type="select" value="ensure"> + <option value="none">none</option> + <option value="ensure">ensure</option> + <option value="reassign">reassign</option> + </param> + <param help="(-out_type) " label="Output file type -- default: determined from file extension or content <br>Note: that not all conversion paths work or make sense" name="param_out_type" optional="True" type="select"> + <option value="mzData">mzData</option> + <option value="mzXML">mzXML</option> + <option value="mzML">mzML</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> + <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"/> + <expand macro="advanced_options"> + <param checked="false" falsevalue="" help="(-TIC_DTA2D) " label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions" name="param_TIC_DTA2D" optional="True" truevalue="-TIC_DTA2D" type="boolean"/> + <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"/> + <param checked="false" falsevalue="" help="(-process_lowmemory) <br>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"/> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + </expand> + </inputs> + <outputs> + <data name="param_out" metadata_source="param_in" format="mgf"> + <change_format> + <when input="param_out_type" value="mzData" format="mzData" /> + <when input="param_out_type" value="mzXML" format="mzXML" /> + <when input="param_out_type" value="mzML" format="mzML" /> + <when input="param_out_type" value="dta2d" format="dta2d" /> + <when input="param_out_type" value="featureXML" format="featureXML" /> + <when input="param_out_type" value="consensusXML" format="consensusXML" /> + <when input="param_out_type" value="edta" format="edta" /> + <when input="param_out_type" value="csv" format="csv" /> + </change_format> </data> - </outputs> - <help>**What it does** - -Converts between different MS file formats. + </outputs> + <help>Converts between different MS file formats. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help> + </tool>