Mercurial > repos > galaxyp > openms_filefilter
diff FileFilter.xml @ 3:59adb20eb08a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
---|---|
date | Wed, 09 Aug 2017 09:52:35 -0400 |
parents | 020fc2600133 |
children | fce0d752c6c5 |
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--- a/FileFilter.xml Thu Apr 27 13:21:46 2017 -0400 +++ b/FileFilter.xml Wed Aug 09 09:52:35 2017 -0400 @@ -1,7 +1,7 @@ <?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="FileFilter" name="FileFilter" version="2.1.0"> +<tool id="FileFilter" name="FileFilter" version="2.2.0"> <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description> <macros> <token name="@EXECUTABLE@">FileFilter</token> @@ -105,6 +105,9 @@ #if $param_peak_options_indexed_file: -peak_options:indexed_file #end if +#if $param_peak_options_zlib_compression: + -peak_options:zlib_compression +#end if #if $param_peak_options_numpress_masstime: -peak_options:numpress:masstime #if " " in str($param_peak_options_numpress_masstime): @@ -338,7 +341,7 @@ #end if </command> <inputs> - <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/> + <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/> <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) "> <option value="mzML">mzML</option> <option value="featureXML">featureXML</option> @@ -420,20 +423,21 @@ <option value="64">64</option> </param> <param name="param_peak_options_indexed_file" display="radio" type="boolean" truevalue="-peak_options:indexed_file" falsevalue="" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file) "/> + <param name="param_peak_options_zlib_compression" display="radio" type="boolean" truevalue="-peak_options:zlib_compression" falsevalue="" checked="false" optional="True" label="Whether to store data with zlib compression (lossless compression)" help="(-zlib_compression) "/> <param name="param_peak_options_numpress_masstime" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) "> <option value="none" selected="true">none</option> <option value="linear">linear</option> <option value="pic">pic</option> <option value="slof">slof</option> </param> - <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" help="(-masstime_error) "/> + <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (default 10 ppm at 100 m/z; set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-masstime_error) "/> <param name="param_peak_options_numpress_intensity" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) "> <option value="none" selected="true">none</option> <option value="linear">linear</option> <option value="pic">pic</option> <option value="slof">slof</option> </param> - <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic)" help="(-intensity_error) "/> + <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-intensity_error) "/> <param name="param_spectra_remove_zoom" display="radio" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/> <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) "> <option value="Unknown">Unknown</option>