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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit e4c2b31a732b57cc0210070afeaa2dfeca1e1eb4 |
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modified:
COPYING taxonomy_krona_chart.xml tool_dependencies.xml |
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added:
test-data/krona_test1.html test-data/taxonomy_data.tax |
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| diff -r bd565e1e3c5f -r 09552faff9c0 COPYING --- a/COPYING Fri Apr 11 12:48:59 2014 -0400 +++ b/COPYING Mon Aug 17 11:36:09 2015 -0400 |
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| @@ -1,7 +1,7 @@ Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ Created by: Paolo Uva <paolo.uva@crs4.it> -Nicola Soranzo <nicola.soranzo@crs4.it> +Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the |
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| diff -r bd565e1e3c5f -r 09552faff9c0 taxonomy_krona_chart.xml --- a/taxonomy_krona_chart.xml Fri Apr 11 12:48:59 2014 -0400 +++ b/taxonomy_krona_chart.xml Mon Aug 17 11:36:09 2015 -0400 |
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| @@ -1,32 +1,113 @@ -<tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0"> +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0"> <description>from taxonomic profile</description> <requirements> - <requirement type="package" version="2.4">kronatools</requirement> + <requirement type="package" version="2.5">krona</requirement> </requirements> <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> <command> - #if $input.ext == 'taxonomy' - ktImportGalaxy "${input}" -o "${output}" - #else - ktImportText "${input}" -o "${output}" - #end if + <![CDATA[ + + #if $type_of_data.input[0].is_of_type('taxonomy'): + + ktImportGalaxy + -a + -d "${type_of_data.max_rank}" + -n "${root_name}" + -o ${output} + ${combine_inputs} + #for $input_count, $input_dataset in enumerate( $type_of_data.input ): + "${input_dataset},${input_count}" + #end for + + #else: + + ktImportText + -a + -n "${root_name}" + -o ${output} + ${combine_inputs} + #for $input_count, $input_dataset in enumerate( $type_of_data.input ): + "${input_dataset},${input_count}" + #end for + + #end if + + ]]> + </command> <inputs> - <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" /> + <conditional name="type_of_data"> + <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text"> + <option value="taxonomy" selected="True">Taxonomy</option> + <option value="text">MetaPhlAn</option> + </param> + <when value="taxonomy"> + <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" /> + <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point"> + <option value="8">Class</option> + <option value="0">Show entire tree</option> + <option value="1">Superkingdom</option> + <option value="2">Kingdom</option> + <option value="3">Subkingdom</option> + <option value="4">Superphylum</option> + <option value="5">Phylum</option> + <option value="6">Subphylum</option> + <option value="7">Superclass</option> + <option value="9">Subclass</option> + <option value="10">Superorder</option> + <option value="11">Order</option> + <option value="12">Suborder</option> + <option value="13">Superfamily</option> + <option value="14">Family</option> + <option value="15">Subfamily</option> + <option value="16">Tribe</option> + <option value="17">Subtribe</option> + <option value="18">Genus</option> + <option value="19">Subgenus</option> + <option value="20">Species</option> + <option value="21">Subspecies</option> + </param> + </when> + <when value="text"> + <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> + </when> + </conditional> + <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> + <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> </inputs> <outputs> <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> </outputs> + <tests> + <test> + <param name="type_of_data_selector" value="taxonomy"/> + <param name="input" value="taxonomy_data.tax" ftype="taxonomy" /> + <param name="max_rank" value="Genus"/> + <param name="root_name" value="Root"/> + <param name="combine_inputs" value="False"/> + <output name="output" file="krona_test1.html" ftype="html" lines_diff="100"/> + </test> + </tests> <help> **What it does** -This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_. -It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools. +This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. + .. _Krona: http://sourceforge.net/p/krona/home/krona/ ------ +**Krona options** + +The Galaxy version supports the following options:: + + -n Name of the highest level. + -c Combine data from each file, rather than creating separate datasets within the chart. + -d Maximum depth of wedges to include in the chart. + +----- + **License and citation** This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. @@ -34,15 +115,14 @@ .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT -If you use this tool in Galaxy, please cite |Cuccuru2014|_. - -.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted -.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135 - -This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_. +You can use this tool only if you agree to the license terms of: `Krona`_. .. _Krona: http://sourceforge.net/p/krona/home/krona/ -.. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385 -.. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385 + + </help> + <citations> + <citation type="doi">10.1186/1471-2105-12-385</citation> + <citation type="doi">10.1093/bioinformatics/btu135</citation> + </citations> </tool> |
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| diff -r bd565e1e3c5f -r 09552faff9c0 test-data/krona_test1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/krona_test1.html Mon Aug 17 11:36:09 2015 -0400 |
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| b'@@ -0,0 +1,6617 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\n+ <head>\n+ <meta charset="utf-8"/>\n+ <link rel="shortcut icon" href="data:image/x-icon;base64,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'..b' <count><val>94</val></count>\n+ <rank><val>family</val></rank>\n+ <node name="Murinae">\n+ <rank><val>subfamily</val></rank>\n+ <count><val>94</val></count>\n+ <node name="Rattus">\n+ <rank><val>genus</val></rank>\n+ <count><val>94</val></count>\n+ <members>\n+ <vals><val>IA_1-296315</val><val>IA_1-322295</val></vals>\n+ </members>\n+ <unassigned><val>2</val></unassigned>\n+ <node name="Rattus norvegicus">\n+ <rank><val>species</val></rank>\n+ <count><val>92</val></count>\n+ <members>\n+ <vals><val>IA_1-144417</val><val>IA_1-278966</val><val>IA_1-314709</val><val>IA_1-324951</val><val>IA_1-27817</val><val>IA_1-95255</val><val>IA_1-104173</val><val>IA_1-135979</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-144996</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-161439</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-216231</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-237681</val><val>IA_1-250166</val><val>IA_1-254274</val><val>IA_1-254274</val><val>IA_1-27817</val><val>IA_1-29000</val><val>IA_1-291427</val><val>IA_1-291427</val><val>IA_1-293054</val><val>IA_1-293054</val><val>IA_1-296315</val><val>IA_1-310974</val><val>IA_1-310974</val><val>IA_1-311282</val><val>IA_1-311282</val><val>IA_1-42600</val><val>IA_1-45102</val><val>IA_1-45102</val><val>IA_1-48105</val><val>IA_1-48105</val><val>IA_1-57254</val><val>IA_1-61975</val><val>IA_1-61975</val><val>IA_1-66943</val><val>IA_1-68288</val><val>IA_1-82334</val><val>IA_1-95526</val></vals>\n+ </members>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ <node name="Bacteria">\n+ <rank><val>superkingdom</val></rank>\n+ <count><val>6</val></count>\n+ <node name="Proteobacteria">\n+ <count><val>6</val></count>\n+ <rank><val>phylum</val></rank>\n+ <node name="Gammaproteobacteria">\n+ <count><val>6</val></count>\n+ <rank><val>class</val></rank>\n+ <node name="Enterobacteriales">\n+ <count><val>6</val></count>\n+ <rank><val>order</val></rank>\n+ <node name="Enterobacteriaceae">\n+ <count><val>6</val></count>\n+ <rank><val>family</val></rank>\n+ <node name="Shigella">\n+ <rank><val>genus</val></rank>\n+ <count><val>6</val></count>\n+ <node name="Shigella flexneri">\n+ <count><val>6</val></count>\n+ <rank><val>species</val></rank>\n+ <members>\n+ <vals><val>IA_1-79371</val><val>IA_1-84488</val><val>IA_1-270826</val><val>IA_1-285361</val><val>IA_1-93958</val><val>IA_1-99821</val></vals>\n+ </members>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+ </node>\n+</node>\n+ </krona>\n+</div></body></html>\n' |
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| diff -r bd565e1e3c5f -r 09552faff9c0 test-data/taxonomy_data.tax --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy_data.tax Mon Aug 17 11:36:09 2015 -0400 |
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| b'@@ -0,0 +1,100 @@\n+IA_1-79371\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604065\n+IA_1-84488\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604065\n+IA_1-270826\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604070\n+IA_1-285361\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604070\n+IA_1-93958\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604070\n+IA_1-99821\t591020\troot\tBacteria\tn\tn\tn\tProteobacteria\tn\tn\tGammaproteobacteria\tn\tn\tEnterobacteriales\tn\tn\tEnterobacteriaceae\tn\tn\tn\tShigella\tn\tShigella flexneri\tn\t281604070\n+IA_1-144417\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604077\n+IA_1-278966\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604077\n+IA_1-314709\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604077\n+IA_1-324951\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604077\n+IA_1-27817\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604153\n+IA_1-95255\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604181\n+IA_1-104173\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-135979\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-139090\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-139090\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-139090\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-144996\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-160446\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-160446\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-160446\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-160446\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognath'..b'a\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-293054\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-293054\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-296315\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-296315\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\n+IA_1-310974\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-310974\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-311282\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-311282\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-322295\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\n+IA_1-42600\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-45102\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-45102\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-48105\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-48105\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-57254\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-61975\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-61975\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-66943\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-68288\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-82334\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n+IA_1-95526\t10116\troot\tEukaryota\tMetazoa\tn\tn\tChordata\tCraniata\tGnathostomata\tMammalia\tn\tEuarchontoglires\tRodentia\tSciurognathi\tn\tMuridae\tMurinae\tn\tn\tRattus\tn\tRattus norvegicus\tn\t281604186\n' |
| b |
| diff -r bd565e1e3c5f -r 09552faff9c0 tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 11 12:48:59 2014 -0400 +++ b/tool_dependencies.xml Mon Aug 17 11:36:09 2015 -0400 |
| b |
| @@ -1,19 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="kronatools" version="2.4"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/krona/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.4.tar</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <!-- ./install.pl must be run inside $INSTALL_DIR . Moreover "change_directory" action does not work because $INSTALL_DIR is outside the defined working directory --> - <action type="shell_command">cd $INSTALL_DIR && ./install.pl --prefix=$INSTALL_DIR</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> + <package name="krona" version="2.5"> + <repository changeset_revision="96d808a49774" name="package_krona_2_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |