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comparison FileFilter.xml @ 3:59adb20eb08a draft

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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
comparison
equal deleted inserted replaced
2:d6878d27f051 3:59adb20eb08a
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 CTD2Galaxy.--> 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 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileFilter" name="FileFilter" version="2.1.0"> 4 <tool id="FileFilter" name="FileFilter" version="2.2.0">
5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description> 5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileFilter</token> 7 <token name="@EXECUTABLE@">FileFilter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
103 #end if 103 #end if
104 #end if 104 #end if
105 #if $param_peak_options_indexed_file: 105 #if $param_peak_options_indexed_file:
106 -peak_options:indexed_file 106 -peak_options:indexed_file
107 #end if 107 #end if
108 #if $param_peak_options_zlib_compression:
109 -peak_options:zlib_compression
110 #end if
108 #if $param_peak_options_numpress_masstime: 111 #if $param_peak_options_numpress_masstime:
109 -peak_options:numpress:masstime 112 -peak_options:numpress:masstime
110 #if " " in str($param_peak_options_numpress_masstime): 113 #if " " in str($param_peak_options_numpress_masstime):
111 "$param_peak_options_numpress_masstime" 114 "$param_peak_options_numpress_masstime"
112 #else 115 #else
336 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window 339 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
337 #end if 340 #end if
338 #end if 341 #end if
339 </command> 342 </command>
340 <inputs> 343 <inputs>
341 <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/> 344 <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/>
342 <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) "> 345 <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) ">
343 <option value="mzML">mzML</option> 346 <option value="mzML">mzML</option>
344 <option value="featureXML">featureXML</option> 347 <option value="featureXML">featureXML</option>
345 <option value="consensusXML">consensusXML</option> 348 <option value="consensusXML">consensusXML</option>
346 </param> 349 </param>
418 <param name="param_peak_options_int_precision" display="radio" type="select" optional="False" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) "> 421 <param name="param_peak_options_int_precision" display="radio" type="select" optional="False" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) ">
419 <option value="32" selected="true">32</option> 422 <option value="32" selected="true">32</option>
420 <option value="64">64</option> 423 <option value="64">64</option>
421 </param> 424 </param>
422 <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) "/> 425 <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) "/>
426 <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) "/>
423 <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) "> 427 <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) ">
424 <option value="none" selected="true">none</option> 428 <option value="none" selected="true">none</option>
425 <option value="linear">linear</option> 429 <option value="linear">linear</option>
426 <option value="pic">pic</option> 430 <option value="pic">pic</option>
427 <option value="slof">slof</option> 431 <option value="slof">slof</option>
428 </param> 432 </param>
429 <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) "/> 433 <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) "/>
430 <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) "> 434 <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) ">
431 <option value="none" selected="true">none</option> 435 <option value="none" selected="true">none</option>
432 <option value="linear">linear</option> 436 <option value="linear">linear</option>
433 <option value="pic">pic</option> 437 <option value="pic">pic</option>
434 <option value="slof">slof</option> 438 <option value="slof">slof</option>
435 </param> 439 </param>
436 <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) "/> 440 <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) "/>
437 <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) "/> 441 <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) "/>
438 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) "> 442 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) ">
439 <option value="Unknown">Unknown</option> 443 <option value="Unknown">Unknown</option>
440 <option value="MassSpectrum">MassSpectrum</option> 444 <option value="MassSpectrum">MassSpectrum</option>
441 <option value="MS1Spectrum">MS1Spectrum</option> 445 <option value="MS1Spectrum">MS1Spectrum</option>