Mercurial > repos > lecorguille > camera_annotate

changeset 3:57dce001024c draft

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Uploaded
author lecorguille
date Wed, 10 Feb 2016 08:49:49 -0500
parents 3cc51ada0ffa
children 47fa258dbbbb
files abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml
diffstat 2 files changed, 11 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/abims_CAMERA_annotateDiffreport.xml	Wed Jan 20 03:41:48 2016 -0500
+++ b/abims_CAMERA_annotateDiffreport.xml	Wed Feb 10 08:49:49 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.2">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -7,7 +7,10 @@
         <requirement type="binary">Rscript</requirement>
         <requirement type="package" version="1.44.0">xcms</requirement>
         <requirement type="package" version="1.22.0">camera</requirement>
-        <requirement type="package" version="2.2.0">camera_w4m_script</requirement>
+        <requirement type="package" version="2.2.1">camera_w4m_script</requirement>
+        <requirement type="binary">CAMERA.r</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="binary">convert</requirement>
     </requirements>
     
     <stdio>
@@ -42,6 +45,7 @@
         #end if
 
         #if $options.option == "show":
+            runDiffreport TRUE
             eicmax $options.eicmax
             eicwidth $options.eicwidth
             value $options.value
@@ -50,15 +54,6 @@
             w $options.w
             mzdec $options.mzdec
             new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
-        #else
-            eicmax 0
-            eicwidth 200
-            value "into"
-            sortpval TRUE 
-            h 480
-            w 640
-            mzdec 2
-            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #end if
         
       
--- a/tool_dependencies.xml	Wed Jan 20 03:41:48 2016 -0500
+++ b/tool_dependencies.xml	Wed Feb 10 08:49:49 2016 -0500
@@ -6,7 +6,10 @@
     <package name="camera" version="1.22.0">
         <repository changeset_revision="e7634e33ca20" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera_w4m_script" version="2.2.0">
-        <repository changeset_revision="26090408d84b" name="package_camera_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="camera_w4m_script" version="2.2.1">
+        <repository changeset_revision="96606d74af08" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="graphicsmagick" version="1.3.20">
+        <repository changeset_revision="25002de17a97" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>