diff OpenSwathDIAPreScoring.xml @ 0:b1af731ae341 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/OpenSwathDIAPreScoring.xml	Wed Mar 01 12:59:14 2017 -0500
@@ -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: [Targeted Experiments]-->
+<tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.1.0">
+  <description>Scoring spectra using the DIA scores.</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathDIAPreScoring
+
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-swath_files
+  #for token in $param_swath_files:
+    $token
+  #end for
+#if $param_min_upper_edge_dist:
+  -min_upper_edge_dist $param_min_upper_edge_dist
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
+    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
+    <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="tabular"/>
+  </outputs>
+  <help>Scoring spectra using the DIA scores.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_OpenSwathDIAPreScoring.html</help>
+</tool>