Mercurial > repos > bebatut > export2graphlan
changeset 0:b344522045f3 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty
| author | bebatut |
|---|---|
| date | Wed, 20 Apr 2016 06:09:29 -0400 |
| parents | |
| children | d7cf3b50a074 |
| files | export2graphlan.xml test-data/annotation_output.txt test-data/input_profile.tabular test-data/tree_output.txt tool_dependencies.xml |
| diffstat | 5 files changed, 522 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export2graphlan.xml Wed Apr 20 06:09:29 2016 -0400 @@ -0,0 +1,215 @@ +<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> + + <description></description> + + <requirements> + <requirement type="package" version="0.16">pandas</requirement> + <requirement type="package" version="0.16">scipy</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + <requirement type="package" version="0.19">export2graphlan</requirement> + </requirements> + + <stdio> + </stdio> + + <version_command> +<![CDATA[ +export2graphlan.py -v +]]> + </version_command> + + <command> +<![CDATA[ + export2graphlan.py + -i $lefse_input + + #if $lefse_output + -o lefse_output + #end if + + -t $tree + -a $annotation + + #if $annotations + --annotations $annotations + #end if + + #if $external_annotations + --external_annotations $external_annotations + #end if + + #if $background_levels + --background_levels $background_levels + #end if + + #if $background_clades + --background_clades "$background_clades" + #end if + + #if $background_colors + --background_colors "$background_colors" + #end if + + #if $title + --title "title" + #end if + + --title_font_size $title_font_size + --def_clade_size $def_clade_size + --min_clade_size $min_clade_size + --max_clade_size $max_clade_size + --def_font_size $def_font_size + --min_font_size $min_font_size + --max_font_size $max_font_size + --annotation_legend_font_size $annotation_legend_font_size + --abundance_threshold $abundance_threshold + + #if $most_abundant + --most_abundant $most_abundant + #end if + + #if $least_biomarkers + --least_biomarkers $least_biomarkers + #end if + + --fname_row $fname_row + --sname_row $sname_row + + #if $metadata_rows + --metadata_rows $metadata_rows + #end if + + #if $skip_rows + --skip_rows $skip_rows + #end if + + #if $sperc + --sperc $sperc + #end if + + #if $fperc + --fperc $fperc + #end if + + #if $stop + --stop $stop + #end if + + #if $ftop + --ftop $ftop + #end if +]]> + </command> + + <inputs> + <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/> + + <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/> + + <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/> + + <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/> + + <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/> + + <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/> + + <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/> + + <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/> + + <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/> + + <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/> + + <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/> + + <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/> + + <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/> + + <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/> + + <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/> + + <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/> + + <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/> + + <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/> + + <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/> + + <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/> + + <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/> + + <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/> + + <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/> + + <param name="sperc" type="float" label="Percentile of sample value + distribution for sample selection (Optional)" help="(--sperc)" + optional="True"/> + + <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/> + + <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/> + + <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/> + </inputs> + + <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="annotation_output.txt"/> + <output name="tree" file="tree_output.txt"/> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format + +In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. + +For more information, check the +`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_. + + ]]></help> + + <citations> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_output.txt Wed Apr 20 06:09:29 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/input_profile.tabular Wed Apr 20 06:09:29 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/tree_output.txt Wed Apr 20 06:09:29 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 20 06:09:29 2016 -0400 @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pandas" version="0.16"> + <repository changeset_revision="ea929a7f2976" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="scipy" version="0.16"> + <repository changeset_revision="80f8536c6dc2" name="package_python_2_7_scipy_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="matplotlib" version="1.4"> + <repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="export2graphlan" version="0.19"> + <install version="1.0"> + <actions> + <action type="shell_command"> + hg clone -r d6c10c1 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>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> + </install> + <readme /> + </package> +</tool_dependency>