comparison macros.xml @ 10:29a4d6e2ae9c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997

9:b86562b4f3fd

<macros>
    <token name="@TOOL_VERSION@">3.0.0a3</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">khmer</xref>
        </xrefs>

  --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 argument="" 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 argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
                <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
                <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
                    label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
            </when>
        </conditional>
    </xml>

        <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} on ${on_string}: 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" token_extension="">
        <collection name="sequences" type="list">
            <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
        </collection>
    </xml>

10:29a4d6e2ae9c

<macros>
    <token name="@TOOL_VERSION@">3.0.0a3</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">khmer</xref>
        </xrefs>

  --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 argument="--max-tablesize" 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 argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
                <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
                <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
                    label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
            </when>
        </conditional>
    </xml>

        <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="csv"
            label="${tool.name} on ${on_string}: k-mer abundance histogram" />
    </xml>
    <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[
 The columns  of the k-mer abundance histogram are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers.
]]></token>

    <xml name="output_sequences" token_extension="">
        <collection name="sequences" type="list">
            <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
        </collection>
    </xml>