# HG changeset patch # User bebatut # Date 1462182260 14400 # Node ID 64e69b47b4ecefca84dee822bbe86a84997dcddd # Parent 5cdaa98d9376acc4857bb6b62a65ff7478659647 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit fe1ede437f1b0e414d84d75e6a607047d1678444-dirty diff -r 5cdaa98d9376 -r 64e69b47b4ec graphlan.xml --- a/graphlan.xml Fri Apr 01 05:51:57 2016 -0400 +++ b/graphlan.xml Mon May 02 05:44:20 2016 -0400 @@ -1,14 +1,18 @@ - + to produce graphical output of an input tree - - biopython - matplotlib - graphlan - + + graphlan_macros.xml + + + + @@ -49,11 +53,9 @@ - + - + @@ -97,23 +99,19 @@ - - + + - + `_. @@ -121,4 +119,4 @@ - \ No newline at end of file + diff -r 5cdaa98d9376 -r 64e69b47b4ec graphlan_annotate.xml --- a/graphlan_annotate.xml Fri Apr 01 05:51:57 2016 -0400 +++ b/graphlan_annotate.xml Mon May 02 05:44:20 2016 -0400 @@ -1,14 +1,18 @@ - + - + for GraPhlAn - - biopython - matplotlib - graphlan - + + graphlan_macros.xml + + + + @@ -30,11 +34,9 @@ - + - + @@ -46,22 +48,18 @@ - + `_. diff -r 5cdaa98d9376 -r 64e69b47b4ec graphlan_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphlan_macros.xml Mon May 02 05:44:20 2016 -0400 @@ -0,0 +1,10 @@ + + + + + biopython + matplotlib + graphlan + + + \ No newline at end of file diff -r 5cdaa98d9376 -r 64e69b47b4ec test-data/intermediary_tree.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/intermediary_tree.txt Mon May 02 05:44:20 2016 -0400 @@ -0,0 +1,439 @@ + + + + + k__Archaea + 1.0 + 58.0748302504 + + p__Euryarchaeota + 1.0 + 58.0748302504 + + c__Methanobacteria + 1.0 + 58.0748302504 + + o__Methanobacteriales + 1.0 + 58.0748302504 + + f__Methanobacteriaceae + 1.0 + 58.0748302504 + + g__Methanobrevibacter + 1.0 + 58.0748302504 + + s__Methanobrevibacter_smithii + 1.0 + 58.0748302504 + + t__Methanobrevibacter_smithii_unclassified + 1.0 + 58.0748302504 + + + + + + + + + + k__Bacteria + 1.0 + 200.0 + + p__Deinococcus_Thermus + 1.0 + 22.298886707 + + c__Deinococci + 1.0 + 22.298886707 + + o__Deinococcales + 1.0 + 22.298886707 + + f__Deinococcaceae + 1.0 + 22.298886707 + + g__Deinococcus + 1.0 + 22.298886707 + + s__Deinococcus_unclassified + 1.0 + 21.1817307606 + + + s__Deinococcus_radiodurans + 1.0 + 21.1340492974 + + t__GCF_000008565 + 1.0 + 21.1340492974 + + + + + + + + + p__Firmicutes + 1.0 + 183.285013514 + #2d19ff + + c__Clostridia + 1.0 + 26.8159954288 + + o__Clostridiales + 1.0 + 26.8159954288 + + f__Clostridiaceae + 1.0 + 26.8159954288 + + g__Clostridium + 1.0 + 26.8159954288 + + s__Clostridium_beijerinckii + 1.0 + 26.8159954288 + + t__Clostridium_beijerinckii_unclassified + 1.0 + 26.8159954288 + + + + + + + + c__Bacilli + 1.0 + 182.398015269 + #2d19ff + + o__Bacillales + 1.0 + 164.332515943 + #2d19ff + + f__Staphylococcaceae + 1.0 + 164.332515943 + #2d19ff + + g__Staphylococcus + 1.0 + 164.332515943 + #2d19ff + + s__Staphylococcus_aureus + 1.0 + 122.793996615 + #2d19ff + + t__Staphylococcus_aureus_unclassified + 1.0 + 122.793996615 + #2d19ff + + + + s__Staphylococcus_epidermidis + 1.0 + 120.392106048 + #2d19ff + + t__Staphylococcus_epidermidis_unclassified + 1.0 + 120.392106048 + #2d19ff + + + + + + + o__Lactobacillales + 1.0 + 96.1062970373 + + f__Streptococcaceae + 1.0 + 96.1062970373 + + g__Streptococcus + 1.0 + 96.1062970373 + + s__Streptococcus_mutans + 1.0 + 93.7375603 + + t__Streptococcus_mutans_unclassified + 1.0 + 93.7375603 + + + + s__Streptococcus_agalactiae + 1.0 + 25.9449465996 + + t__Streptococcus_agalactiae_unclassified + 1.0 + 25.9449465996 + + + + + + + + + p__Actinobacteria + 1.0 + 22.66961905 + + c__Actinobacteria + 1.0 + 22.66961905 + + o__Actinomycetales + 1.0 + 22.66961905 + + f__Propionibacteriaceae + 1.0 + 22.66961905 + + g__Propionibacterium + 1.0 + 22.66961905 + + s__Propionibacterium_acnes + 1.0 + 22.66961905 + + t__Propionibacterium_acnes_unclassified + 1.0 + 22.66961905 + + + + + + + + + p__Proteobacteria + 1.0 + 102.159086265 + #29cc36 + + c__Gammaproteobacteria + 1.0 + 85.4517057547 + + o__Enterobacteriales + 1.0 + 78.466031643 + + f__Enterobacteriaceae + 1.0 + 78.466031643 + + g__Escherichia + 1.0 + 78.466031643 + + s__Escherichia_coli + 1.0 + 58.9341374431 + + t__Escherichia_coli_unclassified + 1.0 + 58.9341374431 + + + + s__Escherichia_unclassified + 1.0 + 49.960616022 + + + + + + o__Pseudomonadales + 1.0 + 34.0879564025 + + f__Moraxellaceae + 1.0 + 20.9013800671 + + g__Acinetobacter + 1.0 + 20.9013800671 + + s__Acinetobacter_baumannii + 1.0 + 20.9013800671 + + t__Acinetobacter_baumannii_unclassified + 1.0 + 20.9013800671 + + + + + + f__Pseudomonadaceae + 1.0 + 33.3271759768 + + g__Pseudomonas + 1.0 + 33.3271759768 + + s__Pseudomonas_unclassified + 1.0 + 28.0078913105 + + + s__Pseudomonas_aeruginosa + 1.0 + 25.8720239085 + + t__Pseudomonas_aeruginosa_unclassified + 1.0 + 25.8720239085 + + + + + + + + c__Alphaproteobacteria + 1.0 + 53.6955516997 + + o__Rhodobacterales + 1.0 + 53.6955516997 + + f__Rhodobacteraceae + 1.0 + 53.6955516997 + + g__Rhodobacter + 1.0 + 53.6955516997 + + s__Rhodobacter_sphaeroides + 1.0 + 53.6955516997 + + t__Rhodobacter_sphaeroides_unclassified + 1.0 + 53.6955516997 + + + + + + + + c__Betaproteobacteria + 1.0 + 20.3264778878 + + o__Neisseriales + 1.0 + 20.3264778878 + + f__Neisseriaceae + 1.0 + 20.3264778878 + + g__Neisseria + 1.0 + 20.3264778878 + + s__Neisseria_meningitidis + 1.0 + 20.3264778878 + + t__Neisseria_meningitidis_unclassified + 1.0 + 20.3264778878 + + + + + + + + c__Epsilonproteobacteria + 1.0 + 20.5761787104 + + o__Campylobacterales + 1.0 + 20.5761787104 + + f__Helicobacteraceae + 1.0 + 20.5761787104 + + g__Helicobacter + 1.0 + 20.5761787104 + + s__Helicobacter_pylori + 1.0 + 20.5761787104 + + t__Helicobacter_pylori_unclassified + 1.0 + 20.5761787104 + + + + + + + + + + 1.5 + 10 + 0.8 + 0.5 + 0.2 + 10 + FIRMICUTES_._._PROTEOBACTERIA + ._._._. + ._._._. + #2d19ff_._._#29cc36 + ._._._. + 40_._._40 + 1 + + \ No newline at end of file diff -r 5cdaa98d9376 -r 64e69b47b4ec test-data/output_image.png Binary file test-data/output_image.png has changed diff -r 5cdaa98d9376 -r 64e69b47b4ec test-data/output_modified_tree.txt --- a/test-data/output_modified_tree.txt Fri Apr 01 05:51:57 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,439 +0,0 @@ - - - - - k__Archaea - 1.0 - 58.0748302504 - - p__Euryarchaeota - 1.0 - 58.0748302504 - - c__Methanobacteria - 1.0 - 58.0748302504 - - o__Methanobacteriales - 1.0 - 58.0748302504 - - f__Methanobacteriaceae - 1.0 - 58.0748302504 - - g__Methanobrevibacter - 1.0 - 58.0748302504 - - s__Methanobrevibacter_smithii - 1.0 - 58.0748302504 - - t__Methanobrevibacter_smithii_unclassified - 1.0 - 58.0748302504 - - - - - - - - - - k__Bacteria - 1.0 - 200.0 - - p__Deinococcus_Thermus - 1.0 - 22.298886707 - - c__Deinococci - 1.0 - 22.298886707 - - o__Deinococcales - 1.0 - 22.298886707 - - f__Deinococcaceae - 1.0 - 22.298886707 - - g__Deinococcus - 1.0 - 22.298886707 - - s__Deinococcus_unclassified - 1.0 - 21.1817307606 - - - s__Deinococcus_radiodurans - 1.0 - 21.1340492974 - - t__GCF_000008565 - 1.0 - 21.1340492974 - - - - - - - - - p__Firmicutes - 1.0 - 183.285013514 - #2d19ff - - c__Clostridia - 1.0 - 26.8159954288 - - o__Clostridiales - 1.0 - 26.8159954288 - - f__Clostridiaceae - 1.0 - 26.8159954288 - - g__Clostridium - 1.0 - 26.8159954288 - - s__Clostridium_beijerinckii - 1.0 - 26.8159954288 - - t__Clostridium_beijerinckii_unclassified - 1.0 - 26.8159954288 - - - - - - - - c__Bacilli - 1.0 - 182.398015269 - #2d19ff - - o__Bacillales - 1.0 - 164.332515943 - #2d19ff - - f__Staphylococcaceae - 1.0 - 164.332515943 - #2d19ff - - g__Staphylococcus - 1.0 - 164.332515943 - #2d19ff - - s__Staphylococcus_aureus - 1.0 - 122.793996615 - #2d19ff - - t__Staphylococcus_aureus_unclassified - 1.0 - 122.793996615 - #2d19ff - - - - s__Staphylococcus_epidermidis - 1.0 - 120.392106048 - #2d19ff - - t__Staphylococcus_epidermidis_unclassified - 1.0 - 120.392106048 - #2d19ff - - - - - - - o__Lactobacillales - 1.0 - 96.1062970373 - - f__Streptococcaceae - 1.0 - 96.1062970373 - - g__Streptococcus - 1.0 - 96.1062970373 - - s__Streptococcus_mutans - 1.0 - 93.7375603 - - t__Streptococcus_mutans_unclassified - 1.0 - 93.7375603 - - - - s__Streptococcus_agalactiae - 1.0 - 25.9449465996 - - t__Streptococcus_agalactiae_unclassified - 1.0 - 25.9449465996 - - - - - - - - - p__Actinobacteria - 1.0 - 22.66961905 - - c__Actinobacteria - 1.0 - 22.66961905 - - o__Actinomycetales - 1.0 - 22.66961905 - - f__Propionibacteriaceae - 1.0 - 22.66961905 - - g__Propionibacterium - 1.0 - 22.66961905 - - s__Propionibacterium_acnes - 1.0 - 22.66961905 - - t__Propionibacterium_acnes_unclassified - 1.0 - 22.66961905 - - - - - - - - - p__Proteobacteria - 1.0 - 102.159086265 - #29cc36 - - c__Gammaproteobacteria - 1.0 - 85.4517057547 - - o__Enterobacteriales - 1.0 - 78.466031643 - - f__Enterobacteriaceae - 1.0 - 78.466031643 - - g__Escherichia - 1.0 - 78.466031643 - - s__Escherichia_coli - 1.0 - 58.9341374431 - - t__Escherichia_coli_unclassified - 1.0 - 58.9341374431 - - - - s__Escherichia_unclassified - 1.0 - 49.960616022 - - - - - - o__Pseudomonadales - 1.0 - 34.0879564025 - - f__Moraxellaceae - 1.0 - 20.9013800671 - - g__Acinetobacter - 1.0 - 20.9013800671 - - s__Acinetobacter_baumannii - 1.0 - 20.9013800671 - - t__Acinetobacter_baumannii_unclassified - 1.0 - 20.9013800671 - - - - - - f__Pseudomonadaceae - 1.0 - 33.3271759768 - - g__Pseudomonas - 1.0 - 33.3271759768 - - s__Pseudomonas_unclassified - 1.0 - 28.0078913105 - - - s__Pseudomonas_aeruginosa - 1.0 - 25.8720239085 - - t__Pseudomonas_aeruginosa_unclassified - 1.0 - 25.8720239085 - - - - - - - - c__Alphaproteobacteria - 1.0 - 53.6955516997 - - o__Rhodobacterales - 1.0 - 53.6955516997 - - f__Rhodobacteraceae - 1.0 - 53.6955516997 - - g__Rhodobacter - 1.0 - 53.6955516997 - - s__Rhodobacter_sphaeroides - 1.0 - 53.6955516997 - - t__Rhodobacter_sphaeroides_unclassified - 1.0 - 53.6955516997 - - - - - - - - c__Betaproteobacteria - 1.0 - 20.3264778878 - - o__Neisseriales - 1.0 - 20.3264778878 - - f__Neisseriaceae - 1.0 - 20.3264778878 - - g__Neisseria - 1.0 - 20.3264778878 - - s__Neisseria_meningitidis - 1.0 - 20.3264778878 - - t__Neisseria_meningitidis_unclassified - 1.0 - 20.3264778878 - - - - - - - - c__Epsilonproteobacteria - 1.0 - 20.5761787104 - - o__Campylobacterales - 1.0 - 20.5761787104 - - f__Helicobacteraceae - 1.0 - 20.5761787104 - - g__Helicobacter - 1.0 - 20.5761787104 - - s__Helicobacter_pylori - 1.0 - 20.5761787104 - - t__Helicobacter_pylori_unclassified - 1.0 - 20.5761787104 - - - - - - - - - - 1.5 - 10 - 0.8 - 0.5 - 0.2 - 10 - FIRMICUTES_._._PROTEOBACTERIA - ._._._. - ._._._. - #2d19ff_._._#29cc36 - ._._._. - 40_._._40 - 1 - - \ No newline at end of file diff -r 5cdaa98d9376 -r 64e69b47b4ec test-data/png_image.png Binary file test-data/png_image.png has changed diff -r 5cdaa98d9376 -r 64e69b47b4ec tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 01 05:51:57 2016 -0400 +++ b/tool_dependencies.xml Mon May 02 05:44:20 2016 -0400 @@ -6,7 +6,7 @@ - +