diff DecoyDatabase.xml @ 0:53f456ded5a6 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DecoyDatabase.xml	Wed Mar 01 12:16:29 2017 -0500
@@ -0,0 +1,88 @@
+<?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="DecoyDatabase" name="DecoyDatabase" version="2.1.0">
+  <description>Create decoy peptide databases from normal ones.</description>
+  <macros>
+    <token name="@EXECUTABLE@">DecoyDatabase</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>DecoyDatabase
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_decoy_string:
+  -decoy_string     "$param_decoy_string"
+#end if
+#if $param_decoy_string_position:
+  -decoy_string_position $param_decoy_string_position
+#end if
+#if $param_append:
+  -append $param_append
+#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="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="(-decoy_string) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
+      <option value="prefix" selected="true">prefix</option>
+      <option value="suffix">suffix</option>
+    </param>
+    <param name="param_append" display="radio" type="select" optional="False" value="true" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
+      <option value="reverse" selected="true">reverse</option>
+      <option value="shuffle">shuffle</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>
+
+   <tests>
+        <test>
+            <param name="param_in" value="DecoyDatabase_input.fasta"/>
+            <output name="param_out" file="DecoyDatabase_output.fasta"/>
+        </test>
+    </tests>
+
+  <help>Create decoy peptide databases from normal ones.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
+</tool>