Mercurial > repos > bgruening > openms
diff FileInfo.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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--- a/FileInfo.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileInfo.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,63 +1,73 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="FileInfo" name="FileInfo" version="1.12.0"> - <description>Shows basic information about the file, such as data ranges and file type.</description> - <macros> - <token name="@EXECUTABLE@">FileInfo</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>FileInfo +<?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="FileInfo" name="FileInfo" version="2.0.0"> + <description>Shows basic information about the file, such as data ranges and file type.</description> + <macros> + <token name="@EXECUTABLE@">FileInfo</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FileInfo --in ${param_in} --in_type ${param_in_type} --out ${param_out} -${param_m} -${param_p} -${param_s} -${param_d} -${param_c} -${param_v} -${param_i} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_tsv: + -out_tsv $param_out_tsv +#end if +#if $param_m: + -m +#end if +#if $param_p: + -p +#end if +#if $param_s: + -s +#end if +#if $param_d: + -d +#end if +#if $param_c: + -c +#end if +#if $param_v: + -v +#end if +#if $param_i: + -i +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -out_tsv ${adv_opts.param_out_tsv} + #if $adv_opts.param_force: + -force +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML,idXML,pepXML" optional="False" label="input file " help="(-in)"/> - <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" 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="idXML">idXML</option> - <option value="pepXML">pepXML</option> - <option value="fid">fid</option> - </param> - <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/> - <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/> - <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s)"/> - <param name="param_d" type="boolean" truevalue="-d true" falsevalue="-d false" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d)"/> - <param name="param_c" type="boolean" truevalue="-c true" falsevalue="-c false" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c)"/> - <param name="param_v" type="boolean" truevalue="-v true" falsevalue="-v false" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v)"/> - <param name="param_i" type="boolean" truevalue="-i true" falsevalue="-i false" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i)"/> - </inputs> - <outputs> - <data name="param_out" label="Optional output file. If left out, the output is written to the command line." format="txt"/> - <data name="param_out_tsv" label="Second optional output file. Tab separated flat text file." format="tabular"/> - </outputs> - <help>**What it does** - -Shows basic information about the file, such as data ranges and file type. + <inputs> + <param format="xml,mzml,mzxml,consensusxml,txt,pepxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/> + <param checked="false" falsevalue="" help="(-m) " label="Show meta information about the whole experiment" name="param_m" optional="True" truevalue="-m" type="boolean"/> + <param checked="false" falsevalue="" help="(-p) " label="Shows data processing information" name="param_p" optional="True" truevalue="-p" type="boolean"/> + <param checked="false" falsevalue="" help="(-s) " label="Computes a five-number statistics of intensities, qualities, and widths" name="param_s" optional="True" truevalue="-s" type="boolean"/> + <param checked="false" falsevalue="" help="(-d) " label="Show detailed listing of all spectra and chromatograms (peak files only)" name="param_d" optional="True" truevalue="-d" type="boolean"/> + <param checked="false" falsevalue="" help="(-c) " label="Check for corrupt data in the file (peak files only)" name="param_c" optional="True" truevalue="-c" type="boolean"/> + <param checked="false" falsevalue="" help="(-v) " label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" name="param_v" optional="True" truevalue="-v" type="boolean"/> + <param checked="false" falsevalue="" help="(-i) " label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" name="param_i" optional="True" truevalue="-i" 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="txt" name="param_out"/> + <data format="tabular" name="param_out_tsv"/> + </outputs> + <help>Shows basic information about the file, such as data ranges and file type. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html</help> + </tool>