diff FeatureLinkerUnlabeled.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerUnlabeled.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,64 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0">
+  <description>Groups corresponding features from multiple maps.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureLinkerUnlabeled
+
+-in ${param_in}
+-out ${param_out}
+${param_keep_subelements}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:second_nearest_gap ${param_second_nearest_gap}
+${param_use_identifications}
+${param_ignore_charge}
+-algorithm:distance_RT:max_difference ${param_max_difference}
+-algorithm:distance_MZ:max_difference ${param_max_difference}
+-algorithm:distance_MZ:unit ${param_unit}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
+    -algorithm:distance_RT:weight ${adv_opts.param_weight}
+    -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
+    -algorithm:distance_MZ:weight ${adv_opts.param_weight}
+    -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
+    -algorithm:distance_intensity:weight ${adv_opts.param_weight}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
+    <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." help="(-keep_subelements)"/>
+    <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
+    <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
+    <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
+    <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
+    <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
+    <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
+      <option value="Da">Da</option>
+      <option value="ppm">ppm</option>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
+      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
+      <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
+      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
+      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
+      <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file" format="consensusXML"/>
+  </outputs>
+  <help>**What it does**
+
+Groups corresponding features from multiple maps.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html
+
+@REFERENCES@
+</help>
+</tool>