Mercurial > repos > galaxyp > openms_baselinefilter
diff BaselineFilter.xml @ 0:4768c361b11f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 13:01:28 -0500 |
parents | |
children | 4e3ec1e5783f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BaselineFilter.xml Wed Mar 01 13:01:28 2017 -0500 @@ -0,0 +1,66 @@ +<?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: [Signal processing and preprocessing]--> +<tool id="BaselineFilter" name="BaselineFilter" version="2.1.0"> + <description>Removes the baseline from profile spectra using a top-hat filter.</description> + <macros> + <token name="@EXECUTABLE@">BaselineFilter</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>BaselineFilter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_struc_elem_length: + -struc_elem_length $param_struc_elem_length +#end if +#if $param_struc_elem_unit: + -struc_elem_unit $param_struc_elem_unit +#end if +#if $param_method: + -method $param_method +#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="mzml" optional="False" label="input raw data file" help="(-in) "/> + <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/> + <param name="param_struc_elem_unit" display="radio" type="select" optional="False" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) "> + <option value="Thomson" selected="true">Thomson</option> + <option value="DataPoints">DataPoints</option> + </param> + <param name="param_method" type="select" optional="False" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default"> + <option value="identity">identity</option> + <option value="erosion">erosion</option> + <option value="dilation">dilation</option> + <option value="opening">opening</option> + <option value="closing">closing</option> + <option value="gradient">gradient</option> + <option value="tophat" selected="true">tophat</option> + <option value="bothat">bothat</option> + <option value="erosion_simple">erosion_simple</option> + <option value="dilation_simple">dilation_simple</option> + </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_out" format="mzml"/> + </outputs> + <help>Removes the baseline from profile spectra using a top-hat filter. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help> +</tool>