Mercurial > repos > lecorguille > camera_annotate

changeset 20:b979ba5888f7 draft

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"planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
author workflow4metabolomics
date Wed, 18 Mar 2020 06:36:02 -0400
parents 01459b73daf9
children 3886548ea1d1
files README.rst abims_CAMERA_annotateDiffreport.xml lib.r
diffstat 3 files changed, 14 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Thu Feb 13 17:23:07 2020 -0500
+++ b/README.rst	Wed Mar 18 06:36:02 2020 -0400
@@ -2,6 +2,10 @@
 Changelog/News
 --------------
 
+**Version 2.2.5+camera1.42.0+galaxy1 - 09/03/2020**
+
+- BUGFIX: Fix the zip export of the pictures (eic and boxplot)
+
 **Version 2.2.5+camera1.42.0 - 13/02/2020**
 
 - UPGRADE: upgrade the xcms version from 3.0.0 to 1.42.0 (see CAMERA News_)
--- a/abims_CAMERA_annotateDiffreport.xml	Thu Feb 13 17:23:07 2020 -0500
+++ b/abims_CAMERA_annotateDiffreport.xml	Wed Mar 18 06:36:02 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5+camera@TOOL_VERSION@+galaxy0">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5+camera@TOOL_VERSION@+galaxy1">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
 
@@ -185,13 +185,13 @@
         </data>
 
         <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
         </data>
         <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
         </data>
         <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter>
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'pdf'</filter>
             <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
         </collection>
 
@@ -436,6 +436,10 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
 
+**Version 2.2.5+camera1.42.0+galaxy1 - 09/03/2020**
+
+- BUGFIX: Fix the zip export of the pictures (eic and boxplot)
+
 @HELP_CAMERA_NEWVERSION_1420@
 
 **Version 2.2.5 - 09/04/2019**
--- a/lib.r	Thu Feb 13 17:23:07 2020 -0500
+++ b/lib.r	Wed Mar 18 06:36:02 2020 -0400
@@ -187,12 +187,12 @@
                     if (args$eicmax != 0) {
                         if (args$png2 == "pdf")
                             diffreport_png2pdf(filebase)
+                        if (args$png2 == "zip")
+                            diffreport_png2zip()
                     }
                 }
             }
         }
-        if (args$png2 == "zip")
-            diffreport_png2zip()
         if (args$tabular2 == "zip")
             diffreport_tabular2zip()
     }