Mercurial > repos > galaxyp > openms_databasefilter
diff DatabaseFilter.xml @ 0:a004cef51e2c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:27:13 -0400 |
parents | |
children | 3d430f968194 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DatabaseFilter.xml Wed Aug 09 09:27:13 2017 -0400 @@ -0,0 +1,56 @@ +<?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: [Utilities]--> +<tool id="DatabaseFilter" name="DatabaseFilter" version="2.2.0"> + <description>Filters a protein database (FASTA format) based on identified proteins</description> + <macros> + <token name="@EXECUTABLE@">DatabaseFilter</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>DatabaseFilter + +#if $param_in: + -in $param_in +#end if +#if $param_id: + -id $param_id +#end if +#if $param_method: + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if +#end if +#if $param_out: + -out $param_out +#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="fasta" optional="False" label="Input FASTA file, containing a database" help="(-in) "/> + <param name="param_id" type="data" format="idxml,mzid" optional="False" label="Input file containing identified peptides and proteins" help="(-id) "/> + <param name="param_method" display="radio" type="select" optional="False" value="whitelist" label="Switch between white-/blacklisting" help="(-method) "> + <option value="whitelist" selected="true">whitelist</option> + <option value="blacklist">blacklist</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="fasta"/> + </outputs> + <help>Filters a protein database (FASTA format) based on identified proteins + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DatabaseFilter.html</help> +</tool>