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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 276a0a0b0457aa7f42c9233c0cf69c09a4970fb1 |
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modified:
macros.xml |
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added:
abundance-dist-single.norm.xml |
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removed:
tool_dependencies.xml |
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| diff -r 69a0d7b6d0d0 -r 8a7203f7b9e7 abundance-dist-single.norm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance-dist-single.norm.xml Fri Sep 11 14:06:04 2015 -0400 |
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| b'@@ -0,0 +1,295 @@\n+<tool id="gedlab-khmer-abundance-dist-single" name="Abundance Distribution (all-in-one)" version="2.0-3">\n+ <description>\n+\t\tCalculate abundance distribution of the k-mers in a given\n+\t\tsequence file.\n+\t</description>\n+ <macros>\n+ <macro name="requirements" type="xml">\n+ <requirements>\n+ <requirement type="package" version="2.0">khmer</requirement>\n+ </requirements>\n+ </macro>\n+ <macro name="version" type="xml">\n+ <version_command>abundance-dist-single.py --version</version_command>\n+ </macro>\n+ <macro name="tableinputs" type="xml">\n+ <conditional name="parameters">\n+ <param help="ksize, n_tables, a specific tablesize" label="Advanced Parameters" name="type" type="select">\n+ <option selected="true" value="simple">\n+\t\t\t\t\tHide\n+\t\t\t\t</option>\n+ <option value="specific">\n+\t\t\t\t\tShow\n+\t\t\t\t</option>\n+ </param>\n+ <when value="simple">\n+ <param display="radio" label="Sample Type" name="tablesize" type="select">\n+ <option selected="true" value="1e9">\n+\t\t\t\t\t\tMicrobial Genome\n+\t\t\t\t\t</option>\n+ <option value="2e9">\n+\t\t\t\t\t\tAnimal Transcriptome\n+\t\t\t\t\t</option>\n+ <option value="4e9">\n+\t\t\t\t\t\tSmall Animal Genome or\n+\t\t\t\t\t\tLow-Diversity Metagenome\n+\t\t\t\t\t</option>\n+ <option value="16e9">\n+\t\t\t\t\t\tLarge Animal Genome\n+\t\t\t\t\t</option>\n+ </param>\n+ </when>\n+ <when value="specific">\n+ <param help="k-mer size to use" label="ksize" name="ksize" type="integer" value="20" />\n+ <param help="number of tables to use" label="n_tables" min="1" name="n_tables" type="integer" value="4" />\n+ <param help="lower bound on the tablesize to use" label="tablesize" name="tablesize_specific" type="text" />\n+ </when>\n+ </conditional>\n+ </macro>\n+ <macro name="input_sequences_filenames" type="xml">\n+ <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" help="Put in order of precedence such as longest reads first." label="FAST[AQ] file(s)" multiple="true" name="inputs" type="data" />\n+ </macro>\n+ <macro name="input_sequence_filename" type="xml">\n+ <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="FAST[AQ] file(s)" name="input_sequence_filename" type="data" />\n+ </macro>\n+ <macro name="input_counting_table_filename" type="xml">\n+ <param format="ct" help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." label="the k-mer counting table to query" name="input_counting_table_filename" type="data" />\n+ </macro>\n+ <macro name="abundance-histogram-output" type="xml">\n+ <data format="txt" label="${tool.name} k-mer abundance histogram. The columns are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers." name="output_histogram_filename">\n+ </data>\n+ </macro>\n+ <macro name="output_sequences" type="xml">\n+ <data format_source="inputs" label="${tool.name} processed nucleotide sequence file" name="output">\n+ <discover_datasets directory="output" pattern="__name__" visible="true" />\n+ </data>\n+ </macro>\n+ <macro name="output_sequences_single" type="xml">\n+ <data format_source="input_sequence_filename" label="${tool.name} processed nucleotide sequence file" name="output" />\n+ </macro>\n+ <macro name="input_zero" type="xml">\n+ <param checked="true" falsevalue="--no-zero" help="Output zero count bins (--no'..b'inputs>\n+ <outputs>\n+ <data format="ct" label="${tool.name} k-mer counting table" name="optional_output_countingtable">\n+ <filter>save_countingtable == True</filter>\n+ </data>\n+ <data format="txt" label="${tool.name} k-mer abundance histogram. The columns are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers." name="output_histogram_filename">\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_sequence_filename" value="test-abund-read-2.fa" />\n+ <param name="type" value="specific" />\n+ <param name="tablesize_specific" value="1e7" />\n+ <param name="n_tables" value="2" />\n+ <param name="ksize" value="17" />\n+ <param name="no_zero" value="false" />\n+ <output name="output_histogram_filename">\n+ <assert_contents>\n+ <has_text text="1,96,96,0.98" />\n+ <has_text text="1001,2,98,1.0" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_sequence_filename" value="test-abund-read-2.fa" />\n+ <param name="type" value="specific" />\n+ <param name="tablesize_specific" value="1e7" />\n+ <param name="n_tables" value="2" />\n+ <param name="ksize" value="17" />\n+ <param name="no_zero" value="false" />\n+ <param name="bigcount" value="false" />\n+ <output name="output_histogram_filename">\n+ <assert_contents>\n+ <has_text text="1,96,96,0.98" />\n+ <has_text text="255,2,98,1.0" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+Calculate the abundance distribution of k-mers from a single sequence file.\n+\n+Note that with `-b` this script is constant memory; in exchange,\n+k-mer counts will stop at 255. The memory usage of this script with\n+`-b` will be about 1.15x the product of the `-x` and\n+`-N` numbers.\n+\n+To count k-mers in multiple files use `load_into_counting.py` and\n+`abundance_dist.py`.\n+\n+ </help>\n+ <citations>\n+ <citation type="bibtex">@article{khmer2015,\n+ author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine\n+ and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,\n+ Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,\n+ Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and\n+ Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah\n+ and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and\n+ Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David\n+ and Lippi, Justin and Mansour, Tamer and McA\'Nulty, Pamela and McDonald, Eric\n+ and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,\n+ Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,\n+ Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and\n+ Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and\n+ Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,\n+ Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and\n+ Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather\n+ L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and\n+ Brown, C. Titus"\n+ title = "The khmer software package: enabling efficient nucleotide\n+ sequence analysis",\n+ year = "2015",\n+ month = "08",\n+ publisher = "F1000",\n+ url = "http://dx.doi.org/10.12688/f1000research.6924.1"\n+ }</citation>\n+ <citation type="doi">10.1371/journal.pone.0101271</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 69a0d7b6d0d0 -r 8a7203f7b9e7 macros.xml --- a/macros.xml Thu Sep 10 19:32:16 2015 -0400 +++ b/macros.xml Fri Sep 11 14:06:04 2015 -0400 |
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| @@ -159,7 +159,19 @@ url = "http://arxiv.org/abs/1203.4802", }</citation></xml> <xml name="graph-citation"> - <citation type="doi">10.1073/pnas.1121464109</citation> + <citation type="bibtex">@article{Pell2012, + doi = {10.1073/pnas.1121464109}, + url = {http://dx.doi.org/10.1073/pnas.1121464109}, + year = {2012}, + month = {jul}, + publisher = {Proceedings of the National Academy of Sciences}, + volume = {109}, + number = {33}, + pages = {13272--13277}, + author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown}, + title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs}, + journal = {Proceedings of the National Academy of Sciences} + }</citation> </xml> <xml name="counting-citation"> <citation type="doi">10.1371/journal.pone.0101271</citation> |
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| diff -r 69a0d7b6d0d0 -r 8a7203f7b9e7 tool_dependencies.xml --- a/tool_dependencies.xml Thu Sep 10 19:32:16 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="khmer" version="2.0"> - <install version="1.0"> - <actions> - <action type="setup_python_environment"> - <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="python" version="2.7" /> - </repository> - <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610abd021254e21b082179a100cd39</package> - </action> - </actions> - </install> - </package> -</tool_dependency> |