# HG changeset patch
# User recetox
# Date 1602664888 0
# Node ID ddcf42d5c99c0a673ddf92c9254485a0d202def1
# Parent  9a1c51cd78998eff7900874f1a672a4621e29036
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit d989bc22c6af869b77be6a366935d4d7a57cf29d"

diff -r 9a1c51cd7899 -r ddcf42d5c99c macros.xml
--- a/macros.xml	Fri Oct 09 08:55:34 2020 +0000
+++ b/macros.xml	Wed Oct 14 08:41:28 2020 +0000
@@ -11,7 +11,7 @@
         </citations>
     </xml>
     <token name="@HELP@"><![CDATA[
-Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid
+**Retip** is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid
 chromatography (HPLC) Mass Spectrometry analysis. Retention time calculation can be useful in identifying
 unknowns and removing false positive annotations. It uses five different machine learning algorithms to built a
 stable, accurate and fast RT prediction model:
diff -r 9a1c51cd7899 -r ddcf42d5c99c retip_filter_rt.xml
--- a/retip_filter_rt.xml	Fri Oct 09 08:55:34 2020 +0000
+++ b/retip_filter_rt.xml	Wed Oct 14 08:41:28 2020 +0000
@@ -5,20 +5,26 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-               /run.sh filter_rt.R '$tolerance' '$input_smiles' 'output_file'
+               /run.sh filter_rt.R --tolerance '$tolerance' --mode '$filtering_mode' '$input_smiles' 'output_file'
       ]]>
     </command>
     <inputs>
-        <param name="tolerance" label="Select Tolerance Value" type="integer" value="" min="0" max="100"
+        <param name="filtering_mode" type="select" label="Filtering Mode">
+            <option value="absolute" selected="True">Absolute</option>
+            <option value="relative">Relative</option>
+            <option value="order">Order</option>
+        </param>
+        <param name="tolerance" label="Tolerance" type="integer" value="30" min="0" max="100"
                help="Value must be between [0 - 100]" optional="false"/>
         <param name="input_smiles" label="Select Input Dataset" type="data" format="h5" optional="false"/>
     </inputs>
     <outputs>
-        <data format="h5" name="output1" label="Predicted RT" from_work_dir="output_file"/>
+        <data format="h5" name="output1" label="Filtered RT" from_work_dir="output_file"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="tolerance" value="10"/>
+            <param name="filtering_mode" value="absolute"/>
+            <param name="tolerance" value="30"/>
             <param name="input_smiles" value="input_rt_filter.h5"/>
             <output name="output1" file="output_rt_filter.h5" ftype="h5" compare="sim_size" delta="50"/>
         </test>
@@ -26,7 +32,15 @@
     <help><![CDATA[
 .. class:: infomark
 
-This tool is used for Predicted Retention Time **Filtering**.
+This tool is used for **Filtering** predicted retention time.
+
+This tool supports three filtering modes:
+
+- absolute (original): only records with \|RT - RTP\| < tolerance pass
+- relative: both RT and RTP are mapped to [0;1] first (independently) and compared on this scale
+- order: only relative order of RT and RTP is taken in account for comparison
+
+In all modes, tolerance is specified in percent.
 
 @HELP@
         ]]>