# HG changeset patch
# User recetox
# Date 1610538154 0
# Node ID d9c9ec0e2bd814bb1a9ae04fa9aec18cfdc5cf86
# Parent  43b60b28ccf733c4c995d0bca0688e229829cb02
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"

diff -r 43b60b28ccf7 -r d9c9ec0e2bd8 ramclustr_csv.xml
--- a/ramclustr_csv.xml	Mon Dec 07 22:14:48 2020 +0000
+++ b/ramclustr_csv.xml	Wed Jan 13 11:42:34 2021 +0000
@@ -10,7 +10,7 @@
     <inputs>
         <expand macro="parameters_csv" />
         <expand macro="parameters_required" />
-        <expand macro="parameters_optional" />
+        <expand macro="parameters_optional_csv" />
     </inputs>
 
     <command detect_errors="aggressive"><![CDATA[
@@ -37,9 +37,7 @@
                 cor_method = "$required.cor_method",
                 rt_only_low_n = $required.rt_only_low_n,
                 replace_zeros = $required.replace_zeros,
-                #if $optional.st
-                    st = $optional.st,
-                #end if
+                st = $ms_csv.st,
                 #if $optional.maxt
                     maxt = $optional.maxt,
                 #end if
diff -r 43b60b28ccf7 -r d9c9ec0e2bd8 ramclustr_macros.xml
--- a/ramclustr_macros.xml	Mon Dec 07 22:14:48 2020 +0000
+++ b/ramclustr_macros.xml	Wed Jan 13 11:42:34 2021 +0000
@@ -8,6 +8,8 @@
             <param label="sample_name_column" name="sample_name_column" type="integer" value="1" help="which column from the csv file contains sample names?" />
             <param label="feature_delimiter" name="feature_delimiter" type="text" value="_" help="Only required if ms input is set! How feature mz and rt are delimited in csv import column header e.g. ='-'" />
             <param label="retention_time_column" name="retention_time_column" type="integer" value="2" help="which position in delimited column header represents the retention time (csv only)" />
+            <param label="st" name="st" type="float" value="1" help="sigma t - time similarity decay value. A recommended starting point is half the value of 
+      your average chromatographic peak width at half max (seconds))." />
         </section>
     </xml>
 
@@ -64,9 +66,17 @@
         </section>
     </xml>
 
-    <xml name="parameters_optional">
+    <xml name="parameters_optional_xcms">
         <section name="optional" title="Optional Parameters" expanded="false">
-            <param label="st" name="st" type="float" optional="true" help="sigma t - time similarity decay value " />
+            <param label="st" name="st" type="float" optional="true" help="sigma t - time similarity decay value. A recommended starting point is half the value of 
+      your average chromatographic peak width at half max (seconds))." />
+            <param label="fftempdir" name="fftempdir" type="text" optional="true" help="valid path: if there are file size limitations on the default ff pacakge temp directory  - getOptions('fftempdir') - you can change the directory used as the fftempdir with this option." />
+            <param label="maxt" name="maxt" type="integer" optional="true" help="maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero" />
+        </section>
+    </xml>
+
+        <xml name="parameters_optional_csv">
+        <section name="optional" title="Optional Parameters" expanded="false">
             <param label="fftempdir" name="fftempdir" type="text" optional="true" help="valid path: if there are file size limitations on the default ff pacakge temp directory  - getOptions('fftempdir') - you can change the directory used as the fftempdir with this option." />
             <param label="maxt" name="maxt" type="integer" optional="true" help="maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero" />
         </section>
diff -r 43b60b28ccf7 -r d9c9ec0e2bd8 ramclustr_wrapper.R
--- a/ramclustr_wrapper.R	Mon Dec 07 22:14:48 2020 +0000
+++ b/ramclustr_wrapper.R	Wed Jan 13 11:42:34 2021 +0000
@@ -83,6 +83,9 @@
     maxt = NULL,
     fftempdir = NULL
 ) {
+    if (!file.exists(idmsms))
+        idmsms <- NULL
+
     x <- RAMClustR::ramclustR(
         ms = ms,
         idmsms = idmsms,