# HG changeset patch # User bgruening # Date 1722010535 0 # Node ID 8c2167481e72837c70397a0e91b320635037d499 # Parent 53dd00a4ab683cee35a67d0a8fd946712d64722c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit d4e8bcb01de330e345970d3df6b75392c7fe2275 diff -r 53dd00a4ab68 -r 8c2167481e72 blobtoolkit.xml --- a/blobtoolkit.xml Tue Mar 28 15:17:19 2023 +0000 +++ b/blobtoolkit.xml Fri Jul 26 16:15:35 2024 +0000 @@ -1,5 +1,5 @@ - genome assembly QC + Genome Assembly QC macros.xml @@ -22,7 +22,14 @@ --taxid $mode_conditional.taxid --taxdump './taxdump' './Blobdir' + && tar -C ./Blobdir -zcvf Blobdir.tgz . + + #else if $mode_conditional.selector == 'plot' + mkdir -p blobtk_files && + tar -xvf '$blobdir_input' -C blobtk_files && + blobtk plot --blobdir blobtk_files --view '$plot_view' + #else if $mode_conditional.selector == 'add' mkdir -p './Blobdir' && mkdir -p './taxdump' && @@ -97,6 +104,11 @@ #end if $mode_conditional.advanced_options.replace './Blobdir' + + #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes' + && blobtk plot --blobdir './Blobdir' --view $blobtk_plot_options.plot_view + #end if + && tar -C ./Blobdir -zcvf Blobdir.tgz . #else if $mode_conditional.selector == 'filter' @@ -156,8 +168,14 @@ #end if ./Blobdir #end if + + #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes' + && blobtk plot --blobdir ./Blobdir --view $blobtk_plot_options.plot_view + #end if + && tar -C ./Blobdir -zcvf Blobdir.tgz . #end if + ]]> @@ -165,6 +183,7 @@ + @@ -217,6 +236,7 @@ +
@@ -295,6 +315,16 @@ [0-9a-zA-Z]+
+ + + + + + + + + + @@ -302,8 +332,18 @@ mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter' + + + (( + (mode_conditional['selector'] == 'add' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or + (mode_conditional['selector'] == 'filter' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or + (mode_conditional['selector'] == 'plot') + )) + + + @@ -314,7 +354,8 @@ - + + @@ -334,9 +375,15 @@ + + + + + + @@ -350,12 +397,16 @@ + + + + @@ -368,12 +419,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4.0.7 - 1 + 2 - genomehubs/blobtoolkit:@TOOL_VERSION@ + quay.io/biocontainers/blobtoolkit:4.3.11 @@ -46,4 +46,21 @@ + + + + + + + + + + + + + + + + + diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/blobdir.tgz Binary file test-data/blobdir.tgz has changed diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.svg Fri Jul 26 16:15:35 2024 +0000 @@ -0,0 +1,660 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.35 + + + +0.40 + + + +0.45 + + + +0.50 + + + +0.55 + + + +0.60 + + + + +gc + + + + + + + + + + + + + + + + + + + + + + + + + + +0.10 + + + +1 + + + +10 + + + +100 + + + + +input_cov + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 + + + +200M + + + +400M + + + +600M + + + + +sum length + + + + + + + +gc + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 + + + +200M + + + +400M + + + +600M + + + + +sum length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Ascomycota + + +[144; 4.68M; 32.8k] + + + + + + + + + + +no-hit + + +[47; 7.65M; 364k] + + + + + + + + + + +Chordata + + +[42; 627M; 29.1M] + + + + + + + + + + +Arthropoda + + +[7; 2.62M; 597k] + + + + + + + + + + +Artverviricota + + +[1; 763k; 763k] + + + + + + + + + + +Nematoda + + +[1; 630k; 630k] + + + + \ No newline at end of file diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output_cumulative.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_cumulative.svg Fri Jul 26 16:15:35 2024 +0000 @@ -0,0 +1,216 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 + + + +25 + + + +50 + + + +75 + + + +100 + + + +125 + + + +150 + + + +175 + + + +200 + + + +225 + + + + +cumulative count + + + + + + + +0 + + + +100M + + + +200M + + + +300M + + + +400M + + + +500M + + + +600M + + + + +cumulative length + + + + + + + + + + + + + + +Ascomycota + + +[144; 4.68M; 32.8k] + + + + + + + + + + +no-hit + + +[47; 7.65M; 364k] + + + + + + + + + + +Chordata + + +[42; 627M; 29.1M] + + + + + + + + + + +Arthropoda + + +[7; 2.62M; 597k] + + + + + + + + + + +Artverviricota + + +[1; 763k; 763k] + + + + + + + + + + +Nematoda + + +[1; 630k; 630k] + + + + \ No newline at end of file diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output_legend.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_legend.svg Fri Jul 26 16:15:35 2024 +0000 @@ -0,0 +1,90 @@ + + + + + + + + + + + + +Ascomycota + + +[144; 4.68M; 32.8k] + + + + + + + + + + +no-hit + + +[47; 7.65M; 364k] + + + + + + + + + + +Chordata + + +[42; 627M; 29.1M] + + + + + + + + + + +Arthropoda + + +[7; 2.62M; 597k] + + + + + + + + + + +Artverviricota + + +[1; 763k; 763k] + + + + + + + + + + +Nematoda + + +[1; 630k; 630k] + + + + \ No newline at end of file diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/test01_blobdir.tar.gz Binary file test-data/test01_blobdir.tar.gz has changed diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/test02_blob.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_blob.svg Fri Jul 26 16:15:35 2024 +0000 @@ -0,0 +1,254 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.50 + + + +0.51 + + + +0.52 + + + +0.53 + + + + +gc + + + + + + + + + + +input_cov + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 + + + +500k + + + +1M + + + +1.5M + + + + +sum length + + + + + + + +gc + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 + + + +500k + + + +1M + + + +1.5M + + + + +sum length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +no-hit + + +[6; 3.2M; 964k] + + + + \ No newline at end of file diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/test02_blobdir.tar.gz Binary file test-data/test02_blobdir.tar.gz has changed