--- a/add_pval_flags.xml	Fri Jun 18 20:23:19 2021 +0000
+++ b/add_pval_flags.xml	Thu Jul 29 20:48:10 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="secimtools_add_pval_flags" name="Add Binary (0/1) -value Flags" version="@WRAPPER_VERSION@">
+<tool id="secimtools_add_pval_flags" name="Add Binary (0/1) P-value Flags" version="@WRAPPER_VERSION@">
   <description>using custom thresholds</description>
   <macros>
       <import>macros.xml</import>
@@ -17,7 +17,7 @@
     <param name="DE_Dataset" type="data" format="tabular" label="Select Dataset containing p-values from your history"/>
     <param name="uniqID" type="text" size="30" value="" label="Unique FeatureID" help="Name of the column in your Dataset that contains unique FeatureIDs."/>
     <param name="pvalue" type="text" size="30" value="" label="P-Value" help="Name of the column containing your p-values."/>
-    <param name="thresholds" type="text" size="30" value="0.1,0.05,0.01" label="P-Value Thresholds" help="Enter the threshold(s). P-values less than the given threshold(s) will be flagged with a 1. Separate more than 1 threshold value with a comma, no spaces allowed."/>
+    <param name="thresholds" type="text" size="30" value="0.1,0.05,0.01" label="P-Value Thresholds" help="Enter the threshold(s). P-values less than the given threshold(s) will be flagged with a 1. Separate more than 1 threshold value with a comma; no spaces allowed. Default values are 0.1,0.05,0.01"/>
   </inputs>
   <outputs>
     <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/>
@@ -25,29 +25,28 @@
   </outputs>
   <tests>
     <test>
-      <param name="DE_Dataset" value="limma_voom_gene_file_01fhl.tsv"/>
-      <param name="uniqID" value="UniqueID"/>
-      <param name="pvalue" value="P.Value"/>
-      <param name="thresholds" value="0.1,0.05,0.01"/>
-      <output name="output" file="add_flags_gene_output_file_01fhl.tsv"/>
-      <output name="flags" file="add_flags_gene_flags_file_01fhl.tsv"/>
-    </test>
-    <test>
-      <param name="DE_Dataset" value="limma_voom_metabolite_file_01fhl.tsv"/>
+      <param name="DE_Dataset" value="limma_voom_gene.tsv"/>
       <param name="uniqID" value="UniqueID"/>
       <param name="pvalue" value="P.Value"/>
       <param name="thresholds" value="0.1,0.05,0.01"/>
-      <output name="output" file="add_flags_metabolite_output_file_01fhl.tsv"/>
-      <output name="flags" file="add_flags_metabolite_flags_file_01fhl.tsv"/>
+      <output name="output" file="add_flags_gene_output.tsv"/>
+      <output name="flags" file="add_flags_gene_flags.tsv"/>
+    </test>
+    <test>
+      <param name="DE_Dataset" value="limma_voom_metabolite.tsv"/>
+      <param name="uniqID" value="UniqueID"/>
+      <param name="pvalue" value="P.Value"/>
+      <param name="thresholds" value="0.1,0.05,0.01"/>
+      <output name="output" file="add_flags_metabolite_output.tsv"/>
+      <output name="flags" file="add_flags_metabolite_flags.tsv"/>
     </test>
   </tests>
   <help><![CDATA[
-
-
 **Tool Description**
 
-  This tool generates an indicator variable (0 or 1) to identify p-values below a user-specified threshold.  A “1” is used to indicate (flag)
-  p-values less than the indicated threshold p-value. The user can flag nominal p-values or p-values after correction for multiple testing.
+ This tool generates 0/1 indicator variables to identify (‘flag’) p-values less than a user-specified threshold or less than the 
+ default values of 0.1, 0.05 and 0.01.  The flag_threshold variable is equal to 1 if the p-value is less than or equal to the 
+ threshold and equal to 0 if greater than the threshold.  You can flag nominal p-values or p-values after correction for multiple testing.
 
 --------------------------------------------------------------------------------
 
@@ -85,7 +84,7 @@
 
   Two output files are generated from the Add Binary (0/1) P-value Flags tool:
 
-**Output File.** A TSV file containing the same columns as the Input Dataset plus an additional column(s) containing 0/1 binary indicators for whether the P-value was less that the user-specified threshold.  The indicator columns are named by appending the user-specified threshold to 'Flag_' prefix (e.g. Flag_user-specified threshold, Flag_0.10).
+**Output File.** A TSV file containing the same columns as the Input Dataset plus an additional column(s) containing 0/1 binary indicators for whether the P-value was less that the user-specified threshold.  The indicator columns are named by appending the user-specified threshold to "Flag" prefix (e.g. Flag_user-specified threshold, Flag_0.10).
 
   +-----------+---------+---------+--------+-------------+-----+
   | FeatureID | p-value | FDR     | Flag_0.2 | Flag_0.05 | ... |
@@ -117,24 +116,19 @@
   | ...       | ...      | ...       | ... |
   +-----------+----------+-----------+-----+
 
-  ]]>
-  </help>
+]]></help>
   <citations>
     <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
     author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
     title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
     journal = {BMC Bioinformatics},
-    year = {in press}
+    year = {2018}
     }</citation>
-    <citation type="bibtex">@article{garcia2010paintomics,
-    title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
-    author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
-    journal={Bioinformatics},
-    volume={27},
-    number={1},
-    pages={137--139},
-    year={2010},
-    publisher={Oxford University Press}
+    <citation type="bibtex">@article{Mor2021GaitGM,
+    title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
+    author={Mor, DE and Huertas, F and Morse, AM and Kaletsky, R and Murphy, CT and Kalia, V and Miller, GW and Moskalenko, O and Conesa, A and McIntyre, LM},
+    journal={BMC Genomics},
+    year={submitted},
     }</citation>
   </citations>
 </tool>