Mercurial > repos > lain > xseekerpreparator

changeset 3:fa97d16330be draft

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" master branch Updating"
author lain
date Thu, 17 Dec 2020 10:13:58 +0000
parents eb7756ab1cbd
children 8cc9fc8eacac
files XSeekerPreparator.xml galaxy/tools/LC-MSMS/XSeekerPreparator.xml
diffstat 2 files changed, 8 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/XSeekerPreparator.xml	Wed Nov 25 13:23:08 2020 +0000
+++ b/XSeekerPreparator.xml	Thu Dec 17 10:13:58 2020 +0000
@@ -1,7 +1,6 @@
 <tool id="xseeker_preparator"
       name="XSeeker Preparator"
       version="1.0.1"
-      profile="20.04"
 >
     <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
     
@@ -11,7 +10,7 @@
     </edam_operations>
     
     <requirements>
-        <requirement type="set_environment">R_SCRIPT_PATH</requirement>
+        <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>
@@ -38,13 +37,12 @@
     </stdio>
 
     <version_command>
-        R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
+        $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
     </version_command>
 
     <command>
         <![CDATA[
-
-            R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
+            $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
 
                 -P
 
@@ -156,7 +154,7 @@
 
 
     <outputs>
-        <data format="xseeker.sqlite" name="output" />
+        <data format="sqlite" name="output" />
     </outputs>
 
     <configfiles>
--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.xml	Wed Nov 25 13:23:08 2020 +0000
+++ b/galaxy/tools/LC-MSMS/XSeekerPreparator.xml	Thu Dec 17 10:13:58 2020 +0000
@@ -1,7 +1,6 @@
 <tool id="xseeker_preparator"
       name="XSeeker Preparator"
       version="1.0.1"
-      profile="20.04"
 >
     <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
     
@@ -11,7 +10,7 @@
     </edam_operations>
     
     <requirements>
-        <requirement type="set_environment">R_SCRIPT_PATH</requirement>
+        <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>
@@ -38,13 +37,12 @@
     </stdio>
 
     <version_command>
-        R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
+        $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
     </version_command>
 
     <command>
         <![CDATA[
-
-            R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
+            $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
 
                 -P
 
@@ -156,7 +154,7 @@
 
 
     <outputs>
-        <data format="xseeker.sqlite" name="output" />
+        <data format="sqlite" name="output" />
     </outputs>
 
     <configfiles>