annotate macros.xml @ 2:5915ca16931b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9

<macros>
    <token name="@WRAPPER_VERSION@">2.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.98">bz2file</requirement>
            <requirement type="package" version="0.9">screed</requirement>
            <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
        </requirements>
    </xml>
    <xml name="version">
        <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" />
        </stdio>
    </xml>
    <token name="@TABLEPARAMS@">
<![CDATA[
#if $parameters.type == "simple"
  --ksize=20
  --n_tables=4
  --max-tablesize=$parameters.tablesize
#else
  --ksize=$parameters.ksize
  --n_tables=$parameters.n_tables
  --max-tablesize="$parameters.tablesize_specific"
#end if
]]>
    </token>
    <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
    <xml name="tableinputs">
        <conditional name="parameters">
            <param name="type" type="select" label="Advanced Parameters"
                help="ksize, n_tables, a specific tablesize" >
                <option value="simple" selected="true">Hide</option>
                <option value="specific">Show</option>
            </param>
            <when value="simple">
                <param name="tablesize" type="select" label="Sample Type" display="radio">
                    <option value="1e9" selected="true">Microbial Genome</option>
                    <option value="2e9">Animal Transcriptome</option>
                    <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
                    <option value="16e9">Large Animal Genome</option>
                </param>
            </when>
            <when value="specific">
                <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
                <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
                <param name="tablesize_specific" type="text" value="1000000.0" 
                    label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
            </when>
        </conditional>
    </xml>
    <xml name="input_sequences_filenames">
        <param  name="inputs" multiple="true" type="data" format="fasta,fastq"
            label="Sequences in FASTA or FASTQ format"
            help="Put in order of precedence such as longest reads first." />
    </xml>
    <xml name="input_sequence_filename">
        <param  name="input_sequence_filename" type="data" format="fasta,fastq"
            label="Sequence in FASTA or FASTQ format" />
    </xml>
    <xml name="input_countgraph_filename">
        <param  name="input_countgraph_filename" type="data" format="oxlicg"
            label="the k-mer countgraph to query"
            help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." />
    </xml>
    <xml name="abundance-histogram-output">
        <data name="output_histogram_filename" 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." />
    </xml>
    <xml name="output_sequences">
        <data name="output" format_source="inputs"
            label="${tool.name} processed nucleotide sequence file">
            <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
        </data>
    </xml>
    <xml name="output_sequences_single">
        <data name="output" format_source="input_sequence_filename"
            label="${tool.name} processed nucleotide sequence file" />
    </xml>
    <xml name="input_zero">
        <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
            help="Output zero count bins (--no-zero)" />
    </xml>
    <xml name="input_bigcount">
        <param  name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
            checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
    </xml>
    <token name="@HELP_FOOTER@"><![CDATA[
(from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token>
    <xml name="software-citation">
        <citation type="bibtex">@article{khmer2015,
     author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
  and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
  Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
  Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
  Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
  and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
  Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
  and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
  and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
  Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
  Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
  Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
  Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
  Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
  Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
  L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
  Brown, C. Titus"
     title = "The khmer software package: enabling efficient nucleotide
  sequence analysis",
     year = "2015",
     month = "08",
     publisher = "F1000",
     url = "http://dx.doi.org/10.12688/f1000research.6924.1"
  }</citation>
    </xml>
    <xml name="diginorm-citation">
        <citation type="bibtex">@unpublished{diginorm,
    author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
Alexis B and Brom, Timothy H",
    title = "A Reference-Free Algorithm for Computational Normalization of
Shotgun Sequencing Data",
    year = "2012",
    eprint = "arXiv:1203.4802",
    url = "http://arxiv.org/abs/1203.4802",
}</citation></xml>
    <xml name="graph-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>
    </xml>
</macros>