# HG changeset patch
# User galaxyp
# Date 1373647208 14400
# Node ID f8356c01939b16600d298bb69215576d30fc6ae7
# Parent  9743296a53a3145933177d7f8e7b809108425426
Uploaded

diff -r 9743296a53a3 -r f8356c01939b psm_eval.xml
--- a/psm_eval.xml	Thu Jun 20 16:21:26 2013 -0400
+++ b/psm_eval.xml	Fri Jul 12 12:40:08 2013 -0400
@@ -66,30 +66,30 @@
     </configfiles>
     <inputs>
         <conditional name="psms_cond">
-            <param name="type" type="select" label="PSMs Type" help="">
+            <param name="type" type="select" label="PSMs Type" help="ProteinPilot Peptide Report inputs results from ProteinPilot search algorithm. mzidentML inputs results from an open source search algorithm">
                 <option value="mzid">MzIdentML (mzid)</option>
                 <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option>
             </param>
             <when value="mzid">
-                <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="" />
+                <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="select appropriate file from history" />
             </when>
             <when value="proteinpilot_peptide_report">
-                <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="" />
+                <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="select appropriate file from history" />
             </when>
         </conditional>
-        <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="" />
-        <param name="output_type" type="select" label="Output Type" help="">
+        <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="select MZML file of experimental MS/MS data" />
+        <param name="output_type" type="select" label="Output Type" help="Tabular is a spreadsheet containing columns of selected properties listed below. (select tabular as the output type and Peptide sequence as the column type. HTML provides visualization of matches (select HTML as the output type and ProtVis Link as the column type)">
             <option value="tsv">Tabular (tsv)</option>
             <option value="html">HTML</option>
         </param>
-        <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" />
-        <param name="mass_type" type="select" label="Mass Type">
+        <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" help="error of precursor ion (in Da). Recommended: 0.5 for LTQ/Orbitrap instrument; 0.01 for HCD/Orbitrap acquisition" />
+        <param name="mass_type" type="select" label="Mass Type" help="Monoisotopic: selects most abundant isotopic MS peak for theoretical mass calculation. Average: uses average mass values for theoretical mass calculation">
             <option value="monoisotopic" selected="true">Monoisotopic</option>
             <option value="average">Average (has known problems)</option>
         </param>
         <repeat name="columns" title="Column">
             <conditional name="column">
-                <param type="select" name="type" label="Column Type">
+                <param type="select" name="type" label="Column Type" help="select features for tabular or HTML output">
                     <option value="peptide">Peptide Sequence</option>
                     <option value="scan_index">Scan Index</option>
                     <option value="scan_number">Scan Number</option>
@@ -232,4 +232,10 @@
             <param name="percent" label="Percent TIC Threshold" type="float" help="Filter all peaks whose intensity does not exceed this percent of total ion current." value="0.02" />
         </macro>
     </macros>
+    <help>
+**What it does**
+
+Generates user-selected metrics in a tabular format for peptide-spectral matches using spectral/peptide summary generated from the search algorithm and mzml input files. The tabular format that is generated can be used for filtering based on user-defined thresholds. Alternatively, it can also provide visualization of peptide-spectral matches, thus allowing further metrics evaluation.
+<help>
 </tool>
+