Mercurial > repos > bebatut > export2graphlan
changeset 3:953621231a6c draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit f20ebff87883fc5639f540418257ca04ce8296fb-dirty
| author | bebatut |
|---|---|
| date | Fri, 01 Apr 2016 05:51:29 -0400 |
| parents | d2b9ea71c6ed |
| children | 4a3676d020e7 |
| files | export2graphlan.xml test-data/input_profile.tabular test-data/output_annotation.txt test-data/output_tree.txt tool_dependencies.xml |
| diffstat | 5 files changed, 309 insertions(+), 5 deletions(-) [+] |
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--- a/export2graphlan.xml Thu Mar 31 04:08:32 2016 -0400 +++ b/export2graphlan.xml Fri Apr 01 05:51:29 2016 -0400 @@ -14,13 +14,13 @@ <version_command> <![CDATA[ -python export2graphlan.py -v +export2graphlan.py -v ]]> </version_command> <command> <![CDATA[ - python export2graphlan.py + export2graphlan.py -i $lefse_input #if $lefse_output @@ -162,11 +162,38 @@ <outputs> <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" /> - </outputs> <tests> <test> + <param name="lefse_input" value="input_profile.tabular"/> + <param name="annotations" value=""/> + <param name="external_annotations" value=""/> + <param name="background_levels" value=""/> + <param name="background_clades" value=""/> + <param name="background_colors" value=""/> + <param name="title" value=""/> + <param name="title_font_size" value="15"/> + <param name="def_clade_size" value="10"/> + <param name="min_clade_size" value="20"/> + <param name="max_clade_size" value="200"/> + <param name="def_font_size" value="10"/> + <param name="min_font_size" value="8"/> + <param name="max_font_size" value="12"/> + <param name="annotation_legend_font_size" value="10"/> + <param name="abundance_threshold" value="20.0"/> + <param name="most_abundant" value=""/> + <param name="least_biomarkers" value=""/> + <param name="fname_row" value="0"/> + <param name="sname_row" value="0" /> + <param name="metadata_rows" value=""/> + <param name="skip_rows" value=""/> + <param name="sperc" value=""/> + <param name="fperc" value=""/> + <param name="stop" value=""/> + <param name="ftop" value=""/> + <output name="annotation" file="output_annotation.txt"/> + <output name="tree" file="output_tree.txt"/> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_profile.tabular Fri Apr 01 05:51:29 2016 -0400 @@ -0,0 +1,83 @@ +#SampleID Metaphlan2_Analysis +k__Bacteria 93.482 +k__Archaea 6.518 +k__Bacteria|p__Firmicutes 73.48655 +k__Bacteria|p__Proteobacteria 19.32463 +k__Archaea|p__Euryarchaeota 6.518 +k__Bacteria|p__Actinobacteria 0.36084 +k__Bacteria|p__Deinococcus_Thermus 0.30999 +k__Bacteria|p__Firmicutes|c__Bacilli 72.54025 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 13.6073 +k__Archaea|p__Euryarchaeota|c__Methanobacteria 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria 5.59702 +k__Bacteria|p__Firmicutes|c__Clostridia 0.9463 +k__Bacteria|p__Actinobacteria|c__Actinobacteria 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci 0.30999 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 0.04347 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales 55.42931 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 17.11093 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales 11.55615 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales 5.59702 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales 2.05115 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales 0.9463 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales 0.30999 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales 0.04347 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae 55.42931 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae 17.11093 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae 11.55615 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae 5.59702 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae 1.93069 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae 0.9463 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae 0.30999 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae 0.12046 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae 0.04347 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus 55.42931 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus 17.11093 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia 11.55615 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter 5.59702 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas 1.93069 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium 0.9463 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus 0.30999 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter 0.12046 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria 0.04347 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_aureus 28.29995 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis 27.12936 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mutans 16.29021 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 6.70485 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter|s__Rhodobacter_sphaeroides 5.59702 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_unclassified 4.8513 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_unclassified 1.12042 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_beijerinckii 0.9463 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae 0.82072 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa 0.81027 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_unclassified 0.15821 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_radiodurans 0.15178 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii 0.12046 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter_pylori 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_meningitidis 0.04347 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_aureus|t__Staphylococcus_aureus_unclassified 28.29995 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis|t__Staphylococcus_epidermidis_unclassified 27.12936 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mutans|t__Streptococcus_mutans_unclassified 16.29021 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__Escherichia_coli_unclassified 6.70485 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__Methanobrevibacter_smithii_unclassified 6.518 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter|s__Rhodobacter_sphaeroides|t__Rhodobacter_sphaeroides_unclassified 5.59702 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_beijerinckii|t__Clostridium_beijerinckii_unclassified 0.9463 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae|t__Streptococcus_agalactiae_unclassified 0.82072 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa|t__Pseudomonas_aeruginosa_unclassified 0.81027 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__Propionibacterium_acnes_unclassified 0.36084 +k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_radiodurans|t__GCF_000008565 0.15178 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii|t__Acinetobacter_baumannii_unclassified 0.12046 +k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter_pylori|t__Helicobacter_pylori_unclassified 0.07684 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_meningitidis|t__Neisseria_meningitidis_unclassified 0.04347
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_annotation.txt Fri Apr 01 05:51:29 2016 -0400 @@ -0,0 +1,107 @@ +clade_separation 0.5 +branch_bracket_depth 0.8 +branch_bracket_width 0.2 +annotation_legend_font_size 10 +class_legend_font_size 10 +class_legend_marker_size 1.5 + +FIRMICUTES annotation FIRMICUTES +FIRMICUTES clade_marker_color #2d19ff +FIRMICUTES clade_marker_size 40 + +PROTEOBACTERIA annotation PROTEOBACTERIA +PROTEOBACTERIA clade_marker_color #29cc36 +PROTEOBACTERIA clade_marker_size 40 + +k__Archaea clade_marker_size 58.0748302504 +p__Euryarchaeota clade_marker_size 58.0748302504 +c__Methanobacteria clade_marker_size 58.0748302504 +o__Methanobacteriales clade_marker_size 58.0748302504 +f__Methanobacteriaceae clade_marker_size 58.0748302504 +g__Methanobrevibacter clade_marker_size 58.0748302504 +s__Methanobrevibacter_smithii clade_marker_size 58.0748302504 +t__Methanobrevibacter_smithii_unclassified clade_marker_size 58.0748302504 +k__Bacteria clade_marker_size 200.0 +p__Actinobacteria clade_marker_size 22.66961905 +c__Actinobacteria clade_marker_size 22.66961905 +o__Actinomycetales clade_marker_size 22.66961905 +f__Propionibacteriaceae clade_marker_size 22.66961905 +g__Propionibacterium clade_marker_size 22.66961905 +s__Propionibacterium_acnes clade_marker_size 22.66961905 +t__Propionibacterium_acnes_unclassified clade_marker_size 22.66961905 +p__Deinococcus_Thermus clade_marker_size 22.298886707 +c__Deinococci clade_marker_size 22.298886707 +o__Deinococcales clade_marker_size 22.298886707 +f__Deinococcaceae clade_marker_size 22.298886707 +g__Deinococcus clade_marker_size 22.298886707 +s__Deinococcus_radiodurans clade_marker_size 21.1340492974 +t__GCF_000008565 clade_marker_size 21.1340492974 +s__Deinococcus_unclassified clade_marker_size 21.1817307606 +p__Firmicutes clade_marker_size 183.285013514 +p__Firmicutes clade_marker_color #2d19ff +c__Bacilli clade_marker_size 182.398015269 +c__Bacilli clade_marker_color #2d19ff +o__Bacillales clade_marker_size 164.332515943 +o__Bacillales clade_marker_color #2d19ff +f__Staphylococcaceae clade_marker_size 164.332515943 +f__Staphylococcaceae clade_marker_color #2d19ff +g__Staphylococcus clade_marker_size 164.332515943 +g__Staphylococcus clade_marker_color #2d19ff +s__Staphylococcus_aureus clade_marker_size 122.793996615 +s__Staphylococcus_aureus clade_marker_color #2d19ff +t__Staphylococcus_aureus_unclassified clade_marker_size 122.793996615 +t__Staphylococcus_aureus_unclassified clade_marker_color #2d19ff +s__Staphylococcus_epidermidis clade_marker_size 120.392106048 +s__Staphylococcus_epidermidis clade_marker_color #2d19ff +t__Staphylococcus_epidermidis_unclassified clade_marker_size 120.392106048 +t__Staphylococcus_epidermidis_unclassified clade_marker_color #2d19ff +o__Lactobacillales clade_marker_size 96.1062970373 +f__Streptococcaceae clade_marker_size 96.1062970373 +g__Streptococcus clade_marker_size 96.1062970373 +s__Streptococcus_agalactiae clade_marker_size 25.9449465996 +t__Streptococcus_agalactiae_unclassified clade_marker_size 25.9449465996 +s__Streptococcus_mutans clade_marker_size 93.7375603 +t__Streptococcus_mutans_unclassified clade_marker_size 93.7375603 +c__Clostridia clade_marker_size 26.8159954288 +o__Clostridiales clade_marker_size 26.8159954288 +f__Clostridiaceae clade_marker_size 26.8159954288 +g__Clostridium clade_marker_size 26.8159954288 +s__Clostridium_beijerinckii clade_marker_size 26.8159954288 +t__Clostridium_beijerinckii_unclassified clade_marker_size 26.8159954288 +p__Proteobacteria clade_marker_size 102.159086265 +p__Proteobacteria clade_marker_color #29cc36 +c__Alphaproteobacteria clade_marker_size 53.6955516997 +o__Rhodobacterales clade_marker_size 53.6955516997 +f__Rhodobacteraceae clade_marker_size 53.6955516997 +g__Rhodobacter clade_marker_size 53.6955516997 +s__Rhodobacter_sphaeroides clade_marker_size 53.6955516997 +t__Rhodobacter_sphaeroides_unclassified clade_marker_size 53.6955516997 +c__Betaproteobacteria clade_marker_size 20.3264778878 +o__Neisseriales clade_marker_size 20.3264778878 +f__Neisseriaceae clade_marker_size 20.3264778878 +g__Neisseria clade_marker_size 20.3264778878 +s__Neisseria_meningitidis clade_marker_size 20.3264778878 +t__Neisseria_meningitidis_unclassified clade_marker_size 20.3264778878 +c__Epsilonproteobacteria clade_marker_size 20.5761787104 +o__Campylobacterales clade_marker_size 20.5761787104 +f__Helicobacteraceae clade_marker_size 20.5761787104 +g__Helicobacter clade_marker_size 20.5761787104 +s__Helicobacter_pylori clade_marker_size 20.5761787104 +t__Helicobacter_pylori_unclassified clade_marker_size 20.5761787104 +c__Gammaproteobacteria clade_marker_size 85.4517057547 +o__Enterobacteriales clade_marker_size 78.466031643 +f__Enterobacteriaceae clade_marker_size 78.466031643 +g__Escherichia clade_marker_size 78.466031643 +s__Escherichia_coli clade_marker_size 58.9341374431 +t__Escherichia_coli_unclassified clade_marker_size 58.9341374431 +s__Escherichia_unclassified clade_marker_size 49.960616022 +o__Pseudomonadales clade_marker_size 34.0879564025 +f__Moraxellaceae clade_marker_size 20.9013800671 +g__Acinetobacter clade_marker_size 20.9013800671 +s__Acinetobacter_baumannii clade_marker_size 20.9013800671 +t__Acinetobacter_baumannii_unclassified clade_marker_size 20.9013800671 +f__Pseudomonadaceae clade_marker_size 33.3271759768 +g__Pseudomonas clade_marker_size 33.3271759768 +s__Pseudomonas_aeruginosa clade_marker_size 25.8720239085 +t__Pseudomonas_aeruginosa_unclassified clade_marker_size 25.8720239085 +s__Pseudomonas_unclassified clade_marker_size 28.0078913105
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_tree.txt Fri Apr 01 05:51:29 2016 -0400 @@ -0,0 +1,82 @@ +k__Archaea +k__Archaea.p__Euryarchaeota +k__Archaea.p__Euryarchaeota.c__Methanobacteria +k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales +k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae +k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter +k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii +k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii.t__Methanobrevibacter_smithii_unclassified +k__Bacteria +k__Bacteria.p__Actinobacteria +k__Bacteria.p__Actinobacteria.c__Actinobacteria +k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales +k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae +k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium +k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes +k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes.t__Propionibacterium_acnes_unclassified +k__Bacteria.p__Deinococcus_Thermus +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans.t__GCF_000008565 +k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_unclassified +k__Bacteria.p__Firmicutes +k__Bacteria.p__Firmicutes.c__Bacilli +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus.t__Staphylococcus_aureus_unclassified +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis +k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis.t__Staphylococcus_epidermidis_unclassified +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae.t__Streptococcus_agalactiae_unclassified +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans +k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans.t__Streptococcus_mutans_unclassified +k__Bacteria.p__Firmicutes.c__Clostridia +k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales +k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae +k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium +k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium.s__Clostridium_beijerinckii +k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium.s__Clostridium_beijerinckii.t__Clostridium_beijerinckii_unclassified +k__Bacteria.p__Proteobacteria +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides +k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides.t__Rhodobacter_sphaeroides_unclassified +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis +k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis.t__Neisseria_meningitidis_unclassified +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori +k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori.t__Helicobacter_pylori_unclassified +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli.t__Escherichia_coli_unclassified +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_unclassified +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii.t__Acinetobacter_baumannii_unclassified +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa.t__Pseudomonas_aeruginosa_unclassified +k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_unclassified \ No newline at end of file
--- a/tool_dependencies.xml Thu Mar 31 04:08:32 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 01 05:51:29 2016 -0400 @@ -15,12 +15,17 @@ <action type="shell_command"> hg clone https://hg@bitbucket.org/CibioCM/export2graphlan </action> + <action type="move_file"> + <source>export2graphlan.py</source> + <destination>$INSTALL_DIR/bin/</destination> + </action> <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> + <source_directory>hclust2</source_directory> + <destination_directory>$INSTALL_DIR/bin/hclust2/</destination_directory> </action> <action type="set_environment"> <environment_variable action="set_to" name="EXPORT2GRAPHLAN_DIR">$INSTALL_DIR/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable> </action> </actions>