diff BaselineFilter.xml @ 0:3070d71e0e5c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BaselineFilter.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,77 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="BaselineFilter" name="BaselineFilter" version="2.0.0">
+  <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="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 $param_struc_elem_unit:
+  -struc_elem_unit
+  #if " " in str($param_struc_elem_unit):
+    "$param_struc_elem_unit"
+  #else
+    $param_struc_elem_unit
+  #end if
+#end if
+#if $param_method:
+  -method
+  #if " " in str($param_method):
+    "$param_method"
+  #else
+    $param_method
+  #end if
+#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_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" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) ">
+      <option value="Thomson">Thomson</option>
+      <option value="DataPoints">DataPoints</option>
+    </param>
+    <param name="param_method" type="select" optional="True" 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">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" 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>**What it does**
+
+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>
+  <expand macro="references"/>
+</tool>