# HG changeset patch
# User lain
# Date 1608209650 0
# Node ID 8cc9fc8eacac695413d868cdd89cdcf6a4674f90
# Parent  fa97d16330bed1da5ddc7696af9ffbc527ff49ed
" master branch Updating"

diff -r fa97d16330be -r 8cc9fc8eacac XSeekerPreparator.xml
--- a/XSeekerPreparator.xml	Thu Dec 17 10:13:58 2020 +0000
+++ b/XSeekerPreparator.xml	Thu Dec 17 12:54:10 2020 +0000
@@ -10,16 +10,19 @@
     </edam_operations>
     
     <requirements>
-        <requirement type="set_environment">R_SCRIPT</requirement>
-        <requirement type="package" version="4.0.0">R</requirement>
-        <requirement type="package" version="1.6.6">optparse</requirement>
-        <requirement type="package" version="3.10.2">xcms</requirement>
-        <requirement type="package" version="1.2.1">blob</requirement>
-        <requirement type="package" version="0.9.4">fst</requirement>
-        <requirement type="package" version="1.4.0">stringr</requirement>
-        <requirement type="package">DBModelR</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
+        <requirement type="package">bioconductor-camera</requirement>
+        <requirement type="package" version="2.29.2">git</requirement> 
+        <requirement type="package" version="4.0">R</requirement>
+        <requirement type="package" version="1.2.1">r-blob</requirement>
+        <requirement type="package" version="1.1.0">r-dbi</requirement>
+        <requirement type="package" version="0.9.4">r-fst</requirement>
+        <requirement type="package" version="1.6.6">r-optparse</requirement>
+        <requirement type="package" version="1.4.0">r-stringr</requirement>
+        <requirement type="package" version="0.3.4">r-purrr</requirement>
+        <requirement type="package" version="2.2.1">r-rsqlite</requirement>
+        <requirement type="package" version="0.1.0">r-dbmodelr</requirement>
     </requirements>
-    
     <stdio>
 
         <exit_code 
@@ -37,12 +40,12 @@
     </stdio>
 
     <version_command>
-        $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
+        Rscript '$__tool_directory__/XSeekerPreparator.R' -v
     </version_command>
 
     <command>
         <![CDATA[
-            $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
+            Rscript '$__tool_directory__/XSeekerPreparator.R'
 
                 -P
 
@@ -50,7 +53,7 @@
                 --output '$output'
 
                 #if $samples.selected
-                    --samples '${",".join(samples.selected)}'
+                    --samples '${",".join($samples.selected)}'
                 #end if
 
                 #if $database.archetypes
@@ -155,6 +158,7 @@
 
     <outputs>
         <data format="sqlite" name="output" />
+        <!-- <data format="xseeker.sqlite" name="output" /> -->
     </outputs>
 
     <configfiles>
diff -r fa97d16330be -r 8cc9fc8eacac galaxy/tools/LC-MSMS/XSeekerPreparator.xml
--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.xml	Thu Dec 17 10:13:58 2020 +0000
+++ b/galaxy/tools/LC-MSMS/XSeekerPreparator.xml	Thu Dec 17 12:54:10 2020 +0000
@@ -10,16 +10,19 @@
     </edam_operations>
     
     <requirements>
-        <requirement type="set_environment">R_SCRIPT</requirement>
-        <requirement type="package" version="4.0.0">R</requirement>
-        <requirement type="package" version="1.6.6">optparse</requirement>
-        <requirement type="package" version="3.10.2">xcms</requirement>
-        <requirement type="package" version="1.2.1">blob</requirement>
-        <requirement type="package" version="0.9.4">fst</requirement>
-        <requirement type="package" version="1.4.0">stringr</requirement>
-        <requirement type="package">DBModelR</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
+        <requirement type="package">bioconductor-camera</requirement>
+        <requirement type="package" version="2.29.2">git</requirement> 
+        <requirement type="package" version="4.0">R</requirement>
+        <requirement type="package" version="1.2.1">r-blob</requirement>
+        <requirement type="package" version="1.1.0">r-dbi</requirement>
+        <requirement type="package" version="0.9.4">r-fst</requirement>
+        <requirement type="package" version="1.6.6">r-optparse</requirement>
+        <requirement type="package" version="1.4.0">r-stringr</requirement>
+        <requirement type="package" version="0.3.4">r-purrr</requirement>
+        <requirement type="package" version="2.2.1">r-rsqlite</requirement>
+        <requirement type="package" version="0.1.0">r-dbmodelr</requirement>
     </requirements>
-    
     <stdio>
 
         <exit_code 
@@ -37,12 +40,12 @@
     </stdio>
 
     <version_command>
-        $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
+        Rscript '$__tool_directory__/XSeekerPreparator.R' -v
     </version_command>
 
     <command>
         <![CDATA[
-            $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
+            Rscript '$__tool_directory__/XSeekerPreparator.R'
 
                 -P
 
@@ -50,7 +53,7 @@
                 --output '$output'
 
                 #if $samples.selected
-                    --samples '${",".join(samples.selected)}'
+                    --samples '${",".join($samples.selected)}'
                 #end if
 
                 #if $database.archetypes
@@ -155,6 +158,7 @@
 
     <outputs>
         <data format="sqlite" name="output" />
+        <!-- <data format="xseeker.sqlite" name="output" /> -->
     </outputs>
 
     <configfiles>