# HG changeset patch
# User iuc
# Date 1708001507 0
# Node ID 1df18470e3d0815c5848b85681ab8e77ea0c7928
# Parent 07164270ec1308d9d0d2b007b0c74b53d3002b75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
diff -r 07164270ec13 -r 1df18470e3d0 dimet_abundance_plot.xml
--- a/dimet_abundance_plot.xml Tue Jan 23 14:57:41 2024 +0000
+++ b/dimet_abundance_plot.xml Thu Feb 15 12:51:47 2024 +0000
@@ -11,7 +11,7 @@
-
+
-
-
-
-
-
-
-
+
@@ -93,7 +88,9 @@
-
+
+
+
@@ -223,9 +220,9 @@
**Available data for testing**
-You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
+You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
files for you are located in the subfolders inside the data folder).
-You can also use the minimal data examples from https://zenodo.org/record/8380706
+You can also use the minimal data examples from https://zenodo.org/record/10579891
]]>
diff -r 07164270ec13 -r 1df18470e3d0 macros.xml
--- a/macros.xml Tue Jan 23 14:57:41 2024 +0000
+++ b/macros.xml Thu Feb 15 12:51:47 2024 +0000
@@ -1,42 +1,46 @@
- 0.1.4
+ 0.2.1
1
pca
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
dimet
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -86,14 +90,14 @@
-
+
+ label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
@@ -115,7 +119,7 @@
+ label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
@@ -139,9 +143,33 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
@@ -167,6 +195,34 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -177,7 +233,7 @@
-
+
@@ -232,7 +288,7 @@
-
+
@@ -307,6 +363,25 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -328,7 +403,7 @@
+ label="Select Metabolite(s) for condition 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list">
@@ -348,8 +423,8 @@
-
+ label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
+
@@ -369,7 +444,7 @@
-
+
@@ -387,27 +462,132 @@
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -420,68 +600,102 @@
]]>
+
+
+
@@ -681,10 +909,43 @@
]]>
+
+
+ 1:
+ #if len($timepoints) > 0:
+ #for $tp in $timepoint:
+ #set $ctrl_found=False
+ #set $ctrl=""
+ #set $comparisons_bis = list()
+
+ #for $co in $conditions:
+ #set $sub_comparisons = list()
+ #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
+ #set $ctrl_found=True
+ #set $ctrl=str($co)
+ #else:
+ $sub_comparisons.append(re.sub('"', '', str($co)))
+ $sub_comparisons.append(re.sub('"', '', str($tp)))
+
+ #end if
+ $comparisons_bis.append($sub_comparisons)
+ #end for
+
+ #if $ctrl_found:
+ $sub_comparisons.append(str($ctrl))
+ $sub_comparisons.append(str($tp))
+ $comparisons_bis.append($sub_comparisons)
+ #end if
+
+ $comparisons.append($comparisons_bis)
+ #end for
+ #else
+ #for $co in $conditions:
+ $comparisons.append(re.sub('"', '', str($co)))
+ #end for
+ #end if
+
+ #else
+ #if len($conditions) > 0:
+ #if len($timepoints) > 1:
+ #for $co in $conditions:
+ #set $comparisons_bis = list()
+ #for $tp in $timepoint:
+ #set $sub_comparisons = list()
+ $sub_comparisons.append(re.sub('"', '', str($co)))
+ $sub_comparisons.append(re.sub('"', '', str($tp)))
+ $comparisons_bis.append($sub_comparisons)
+ #end for
+ $comparisons.append($comparisons_bis)
+ #end for
+ #end if
+ #else
+ #for $tp in $timepoint:
+ $comparisons.append(re.sub('"', '', str($tp)))
+ #end for
+ #end if
+ #end if
+ ]]>