# HG changeset patch # User iuc # Date 1708001354 0 # Node ID 23f87b8cc62bd269aaaa67c0267d4f86d3663b18 # Parent a06d1febf79e809422537b817f48192bd4dfd2b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f diff -r a06d1febf79e -r 23f87b8cc62b dimet_pca_plot.xml --- a/dimet_pca_plot.xml Tue Jan 23 14:59:40 2024 +0000 +++ b/dimet_pca_plot.xml Thu Feb 15 12:49:14 2024 +0000 @@ -233,9 +233,9 @@ **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 a06d1febf79e -r 23f87b8cc62b macros.xml --- a/macros.xml Tue Jan 23 14:59:40 2024 +0000 +++ b/macros.xml Thu Feb 15 12:49:14 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 + ]]>