diff SpecLibCreator.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

--- a/SpecLibCreator.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/SpecLibCreator.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,37 +1,60 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="SpecLibCreator" name="SpecLibCreator" version="1.12.0">
-  <description>Creates an MSP formatted spectral library.</description>
-  <macros>
-    <token name="@EXECUTABLE@">SpecLibCreator</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>SpecLibCreator
+<?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="SpecLibCreator" name="SpecLibCreator" version="2.0.0">
+    <description>Creates an MSP formatted spectral library.</description>
+    <macros>
+      <token name="@EXECUTABLE@">SpecLibCreator</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>SpecLibCreator
 
--info ${param_info}
--itemseperator ${param_itemseperator}
-${param_itemenclosed}
--spec ${param_spec}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_info:
+  -info $param_info
+#end if
+#if $param_itemseperator:
+  -itemseperator     &quot;$param_itemseperator&quot;
+#end if
+#if $param_itemenclosed:
+  -itemenclosed
+#end if
+#if $param_spec:
+  -spec $param_spec
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc." help="(-info)"/>
-    <param name="param_itemseperator" type="text" size="20" value="," label=" Seperator between items. e.g. ," help="(-itemseperator)"/>
-    <param name="param_itemenclosed" type="boolean" truevalue="-itemenclosed true" falsevalue="-itemenclosed false" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed e.g. '$peptide$,$run$..." help="(-itemenclosed)"/>
-    <param name="param_spec" type="data" format="mzXML" optional="False" label="spectra" help="(-spec)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output MSP formated spectra library" format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Creates an MSP formatted spectral library.
+    <inputs>
+      <param format="tabular" help="(-info) " label="Holds id, peptide, retention time etc" name="param_info" optional="False" type="data"/>
+      <param help="(-itemseperator) " label=" Seperator between items. e.g. ," name="param_itemseperator" size="30" type="text" value=",">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param checked="false" falsevalue="" help="(-itemenclosed) e.g. '$peptide$,$run$" label="'true' or 'false' if true every item is enclosed" name="param_itemenclosed" optional="True" truevalue="-itemenclosed" type="boolean"/>
+      <param format="xml,mzxml" help="(-spec) " label="spectra" name="param_spec" optional="False" type="data"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="txt" name="param_out"/>
+    </outputs>
+    <help>Creates an MSP formatted spectral library.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html</help>
+  </tool>