diff DatabaseFilter.xml @ 0:0617defc2f4d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DatabaseFilter.xml	Fri Jul 14 18:39:34 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>