Mercurial > repos > bgruening > openms
diff 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 |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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--- a/TextExporter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TextExporter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,71 +1,137 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="TextExporter" name="TextExporter" version="1.12.0"> - <description>Exports various XML formats to a text file.</description> - <macros> - <token name="@EXECUTABLE@">TextExporter</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>TextExporter +<?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 --in ${param_in} --out ${param_out} --separator ${param_separator} --replacement ${param_replacement} --quoting ${param_quoting} -${param_no_ids} --threads \${GALAXY_SLOTS:-24} -${param_minimal} -${param_proteins_only} -${param_peptides_only} -${param_first_dim_rt} --consensus:centroids ${param_centroids} --consensus:elements ${param_elements} --consensus:features ${param_features} --consensus:sorting_method ${param_sorting_method} -${param_sort_by_maps} -${param_sort_by_size} +#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 name="param_in" type="data" format="featureXML,consensusXML,idXML,mzML" optional="False" label="Input file " help="(-in)"/> - <param name="param_separator" type="text" size="20" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator)"/> - <param name="param_replacement" type="text" size="20" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement)"/> - <param name="param_quoting" type="select" optional="True" value="none" 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" help="(-quoting)"> - <option value="none">none</option> - <option value="double">double</option> - <option value="escape">escape</option> - </param> - <param name="param_no_ids" type="boolean" truevalue="-no_ids true" falsevalue="-no_ids false" checked="false" optional="True" label="Supresses output of identification data." help="(-no_ids)"/> - <param name="param_minimal" type="boolean" truevalue="-feature:minimal true" falsevalue="-feature:minimal false" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity." help="(-minimal)"/> - <param name="param_proteins_only" type="boolean" truevalue="-id:proteins_only true" falsevalue="-id:proteins_only false" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only)"/> - <param name="param_peptides_only" type="boolean" truevalue="-id:peptides_only true" falsevalue="-id:peptides_only false" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only)"/> - <param name="param_first_dim_rt" type="boolean" truevalue="-id:first_dim_rt true" falsevalue="-id:first_dim_rt false" checked="false" optional="True" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)." help="(-first_dim_rt)"/> - <param name="param_sorting_method" type="select" optional="True" value="none" label="Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method" help="(-sorting_method)"> - <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 name="param_sort_by_maps" type="boolean" truevalue="-consensus:sort_by_maps true" falsevalue="-consensus:sort_by_maps false" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps)"/> - <param name="param_sort_by_size" type="boolean" truevalue="-consensus:sort_by_size true" falsevalue="-consensus:sort_by_size false" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size)"/> - </inputs> - <outputs> - <data name="param_out" label="Output file (mandatory for featureXML and idXML)" format="tabular"/> - <data name="param_centroids" label="Output file for centroids of consensus features" format="tabular"/> - <data name="param_elements" label="Output file for elements of consensus features" format="tabular"/> - <data name="param_features" label="Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)" format="tabular"/> - </outputs> - <help>**What it does** - -Exports various XML formats to a text file. + <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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html</help> + </tool>