--- a/encyclopedia_quantify.xml	Wed Aug 19 08:38:25 2020 -0400
+++ b/encyclopedia_quantify.xml	Fri Aug 21 16:11:54 2020 -0400
@@ -46,13 +46,11 @@
         <param name="select_outputs" type="select" label="Select outputs" multiple="true">
             <option value="log" selected="true">log</option>
             <option value="elib" selected="true">elib</option>
-            <option value="features" selected="true">concatenated_features.txt</option>
+            <option value="features" selected="false">concatenated_features.txt</option>
             <option value="results" selected="true">concatenated_results.txt</option>
             <option value="decoy" selected="false">concatenated_decoy.txt</option>
-            <!--
             <option value="rt_plots" selected="false">Retention Time Plots</option>
             <option value="rt_tables" selected="false">Retention Time Tables</option>
-            -->
             <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
             <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
         </param>
@@ -82,16 +80,14 @@
                 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
             </actions>
         </data>
-        <!--
         <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
-            <filter>l and 'rt_plots' in select_outputs</filter>
+            <filter>library and 'rt_plots' in select_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
         </collection>
         <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
-            <filter>l and 'rt_tables' in select_outputs</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
+            <filter>library and 'rt_tables' in select_outputs</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.mzML\..+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
         </collection>
-        -->
         <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
             <filter>a and 'peptides' in select_outputs</filter>
             <actions>
@@ -130,8 +126,31 @@
 
 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. 
 
+
+**Inputs**
+
+  - Spectrum files in mzML format
+  - A chromatogram library that can be generated by SearchToLib
+  - A protein data base in fasta format
+
 @MSCONVERT_HELP@
 
+**Outputs**
+
+  - A log file
+  - A Chromatogram Library (.elib)
+  - The identified features in tabular format
+    Feature values of scans that are used by percolator to determine matches.
+  - The identified Peptide Spectral Match results in tabular format
+    Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
+  - The identified peptides in tabular format
+    Per peptide: the normalized intensity for each scan file.
+    Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
+  - The identified proteins in tabular format
+    Per protein: the normalized intensity for each scan file.
+    Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
+
+
 **Typical DIA SearchToLib Workflow**
 
 Two sets of Mass Spec MS/MS DIA data are collected for the experiment.  In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments.

--- a/macros.xml	Wed Aug 19 08:38:25 2020 -0400
+++ b/macros.xml	Fri Aug 21 16:11:54 2020 -0400
@@ -128,7 +128,7 @@
     <token name="@LINK_LIB_INPUT@"><![CDATA[
     #if $library
     #set $l_name = $ln_name($library)
-    cp '$library' $l_name &&
+    cp '$library' '$l_name' &&
     #else
     #set $l_name = None
     #end if
@@ -494,7 +494,7 @@
     </token>
     <token name="@MSCONVERT_HELP@"><![CDATA[
 
-    The MSConvert command can be used to deconvolute DIA raw files. You need to use these options
+    The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:
 
     ::