Mercurial > repos > galaxyp > openms_dtaextractor
diff DTAExtractor.xml @ 0:8d5dc126d30b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:59:45 -0500 |
| parents | |
| children | a8422a1cc55c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DTAExtractor.xml Wed Mar 01 12:59:45 2017 -0500 @@ -0,0 +1,82 @@ +<?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="DTAExtractor" name="DTAExtractor" version="2.1.0"> + <description>Extracts spectra of an MS run file to several files in DTA format.</description> + <macros> + <token name="@EXECUTABLE@">DTAExtractor</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>DTAExtractor + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out "$param_out" +#end if +#if $param_mz: + -mz "$param_mz" +#end if +#if $param_rt: + -rt "$param_rt" +#end if +#if $param_level: + -level "$param_level" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +> $param_stdout +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> + <param name="param_out" type="text" size="30" label="base name of DTA output files (RT, m/z and extension are appended)" help="(-out) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_mz" type="text" size="30" value=":" label="m/z range of precursor peaks to extract" help="(-mz) <br>This option is ignored for MS level 1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_rt" type="text" size="30" value=":" label="retention time range of spectra to extract" help="(-rt) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_level" type="text" size="30" value="1,2,3" label="MS levels to extract" help="(-level) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>Extracts spectra of an MS run file to several files in DTA format. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_DTAExtractor.html</help> +</tool>