--- a/pmd_fdr.xml	Tue Oct 01 08:54:39 2019 -0400
+++ b/pmd_fdr.xml	Mon Oct 07 11:59:13 2019 -0400
@@ -1,41 +1,30 @@
 <tool id="pmd_fdr" name="PMD FDR" version="0.1.0">
     <description>recalculate FDR fom precursor mass discrepancy</description>
     <requirements>
-        <requirement type="package" version="">R</requirement>
-        <requirement type="package" version="">r-stringr</requirement>
-        <requirement type="package" version="">r-argparser</requirement>
-        <requirement type="package" version="">r-codetools</requirement>
-        <requirement type="package" version="">r-runit</requirement>
+        <requirement type="package" version="3.5.1">r-base</requirement>
+        <requirement type="package" version="1.4.0">r-stringr</requirement>
+        <requirement type="package" version="0.4">r-argparser</requirement>
+        <requirement type="package" version="0.2-16">r-codetools</requirement>
+        <requirement type="package" version="0.4.32">r-runit</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R' 
         --psm_report '$psm_report'
         #if $psm_report_1_percent:
           --psm_report_1_percent '$psm_report_1_percent'
         #end if
         --input_file_type $input_file_type 
-        --score_field_name "$score_field_name"
         --output_g_fdr '$output_g_fdr'
         --output_i_fdr '$output_i_fdr'
         --output_densities '$output_densities'
     ]]></command>
     <inputs>
-        <param argument="--psm_report" type="data" format="tabular" label="PSM report"/>
-        <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR" optional="true"/>
+        <param argument="--psm_report" type="data" format="tabular" label="PSM report (Peptide Spectrum Match)"/>
+        <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR (Optional)" optional="true"/>
         <param argument="--input_file_type" type="select" label="Input file type">
-            <option value="PSM_Report" selected="true">PSM_Report</option>
+            <option value="PSM_Report" selected="true">PeptideShaker PSM_Report</option>
             <option value="PMD_FDR_input_file">PMD_FDR_input_file</option>
         </param>
-        <param argument="--score_field_name" type="text" value="" label="Score Field name in PSM Report header line">
-            <validator type="empty_field"/>
-            <sanitizer>
-                <valid initial="string.printable">
-                </valid>
-            </sanitizer>
-        </param>
     </inputs>
     <outputs>
         <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/>
@@ -45,32 +34,37 @@
     <tests>
         <test>
             <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/>
-            <param name="score_field_name" value="Confidence [%]"/>
             <output name="output_g_fdr" file="output_g_fdr.tabular" />
             <output name="output_i_fdr" file="output_i_fdr.tabular" />
             <output name="output_densities" file="output_densities.tabular" />
         </test>
     </tests>
     <help><![CDATA[
+Computes individual and global False Discovery Rate (FDR) using Precursor Mass Discrepancy (PMD) from a Peptide Spectrum Match (PSM) report.  
+
+The PSM report must be from PeptideShaker (--input_file_type PSM_Report), 
+or otherwise (--input_file_type PMD_FDR_input_file) have columns with header names:
+
+  - PMD_FDR_input_score
+  - PMD_FDR_pmd
+  - PMD_FDR_spectrum_file
+  - PMD_FDR_proteins
+  - PMD_FDR_spectrum_title
+  - PMD_FDR_sequence
+  - PMD_FDR_decoy
+
+
 PMD_FDR_package_for_Galaxy.R
 
 usage: PMD_FDR_package_for_Galaxy.R [--] [--help] [--opts OPTS] [--psm_report PSM_REPORT] [--psm_report_1_percent PSM_REPORT_1_PERCENT] [--output_i_fdr OUTPUT_I_FDR] [--output_g_fdr OUTPUT_G_FDR] [--output_densities OUTPUT_DENSITIES] [--score_field_name SCORE_FIELD_NAME] [--input_file_type INPUT_FILE_TYPE]
 
-Computes individual and global FDR using Precursor Mass Discrepancy (PMD-FDR)
-
-
-flags:
-  -h, --help            show this help message and exit
-
-optional arguments:
-  -x, --opts OPTS            RDS file containing argument values
+arguments:
   -p, --psm_report PSM_REPORT            full name and path to the PSM report
   --psm_report_1_percent PSM_REPORT_1_PERCENT            full name and path to the PSM report for 1% FDR [default: ]
+  -i, --input_file_type INPUT_FILE_TYPE            type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
   -o, --output_i_fdr OUTPUT_I_FDR            full name and path to the i-FDR output file  [default: ]
   --output_g_fdr OUTPUT_G_FDR            full name and path to the g-FDR output file  [default: ]
   --output_densities OUTPUT_DENSITIES            full name and path to the densities output file  [default: ]
-  -s, --score_field_name SCORE_FIELD_NAME            name of score field (in R format) [default: ]
-  -i, --input_file_type INPUT_FILE_TYPE            type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
 
     ]]></help>
 </tool>