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view TextExporter.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author | bgruening |
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date | Wed, 27 Jan 2016 10:06:49 -0500 |
parents | 3d84209d3178 |
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<?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="TextExporter" name="TextExporter" version="2.0.0"> <description>Exports various XML formats to a text file.</description> <macros> <token name="@EXECUTABLE@">TextExporter</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>TextExporter #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_separator: -separator "$param_separator" #end if #if $param_replacement: -replacement "$param_replacement" #end if #if $param_quoting: -quoting #if " " in str($param_quoting): "$param_quoting" #else $param_quoting #end if #end if #if $param_no_ids: -no_ids #end if -threads \${GALAXY_SLOTS:-24} #if $param_feature_minimal: -feature:minimal #end if #if $param_feature_add_metavalues: -feature:add_metavalues $param_feature_add_metavalues #end if #if $param_id_proteins_only: -id:proteins_only #end if #if $param_id_peptides_only: -id:peptides_only #end if #if $param_id_first_dim_rt: -id:first_dim_rt #end if #if $param_consensus_centroids: -consensus:centroids $param_consensus_centroids #end if #if $param_consensus_elements: -consensus:elements $param_consensus_elements #end if #if $param_consensus_features: -consensus:features $param_consensus_features #end if #if $param_consensus_sorting_method: -consensus:sorting_method #if " " in str($param_consensus_sorting_method): "$param_consensus_sorting_method" #else $param_consensus_sorting_method #end if #end if #if $param_consensus_sort_by_maps: -consensus:sort_by_maps #end if #if $param_consensus_sort_by_size: -consensus:sort_by_size #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param format="xml,consensusxml,mzml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/> <param help="(-separator) " label="The used separator character(s); if not set the 'tab' character is used" name="param_separator" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-replacement) " label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" name="param_replacement" size="30" type="text" value="_"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-quoting) " label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, <br>'escape' for quoting with backslash-escaping of embedded quotes" name="param_quoting" optional="True" type="select" value="none"> <option value="none">none</option> <option value="double">double</option> <option value="escape">escape</option> </param> <param checked="false" falsevalue="" help="(-no_ids) " label="Suppresses output of identification data" name="param_no_ids" optional="True" truevalue="-no_ids" type="boolean"/> <param checked="false" falsevalue="" help="(-minimal) " label="Set this flag to write only three attributes: RT, m/z, and intensity" name="param_feature_minimal" optional="True" truevalue="-feature:minimal" type="boolean"/> <param help="(-add_metavalues) Set to -1 to omit meta values (default)" label="Add columns for meta values which occur with a certain frequency (0-100%)" max="100" min="-1" name="param_feature_add_metavalues" optional="True" type="integer" value="-1"/> <param checked="false" falsevalue="" help="(-proteins_only) " label="Set this flag if you want only protein information from an idXML file" name="param_id_proteins_only" optional="True" truevalue="-id:proteins_only" type="boolean"/> <param checked="false" falsevalue="" help="(-peptides_only) " label="Set this flag if you want only peptide information from an idXML file" name="param_id_peptides_only" optional="True" truevalue="-id:peptides_only" type="boolean"/> <param checked="false" falsevalue="" help="(-first_dim_rt) " label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" name="param_id_first_dim_rt" optional="True" truevalue="-id:first_dim_rt" type="boolean"/> <param help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method" label="Sorting options can be combined" name="param_consensus_sorting_method" optional="True" type="select" value="none"> <option value="none">none</option> <option value="RT">RT</option> <option value="MZ">MZ</option> <option value="RT_then_MZ">RT_then_MZ</option> <option value="intensity">intensity</option> <option value="quality_decreasing">quality_decreasing</option> <option value="quality_increasing">quality_increasing</option> </param> <param checked="false" falsevalue="" help="(-sort_by_maps) " label="Apply a stable sort by the covered maps, lexicographically" name="param_consensus_sort_by_maps" optional="True" truevalue="-consensus:sort_by_maps" type="boolean"/> <param checked="false" falsevalue="" help="(-sort_by_size) " label="Apply a stable sort by decreasing size (i.e., the number of elements)" name="param_consensus_sort_by_size" optional="True" truevalue="-consensus:sort_by_size" type="boolean"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> </expand> </inputs> <outputs> <data format="tabular" name="param_out"/> <data format="tabular" name="param_consensus_centroids"/> <data format="tabular" name="param_consensus_elements"/> <data format="tabular" name="param_consensus_features"/> </outputs> <help>Exports various XML formats to a text file. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html</help> </tool>