comparison macros.xml @ 60:fe697e0cb24a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty

59:08a599cf71d0

<macros>
	<xml name="requirements">
		<requirements>
			<!-- <requirement type="binary">@BINARY@</requirement> -->
			<requirement type="package" version="1.1">khmer</requirement>
		</requirements>
		<version_command>@BINARY@ --version</version_command>
	</xml>
	<token name="@TABLEPARAMS@">#if $parameters.type == "simple"
  --ksize=20
  --n_tables=4
  --min-tablesize=$parameters.tablesize
#else
  --ksize=$parameters.ksize
  --n_tables=$parameters.n_tables
  --min-tablesize=$parameters.tablesize_specific
  #end if</token>
	<token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
	<xml name="tableinputs">
		<conditional name="parameters">
			<param	name="type"

                        label="the k-mer counting table 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 counting table." />
	</xml>
	<xml name="abundance-histogram-output">
                <data   name="output_histogram_filename"
                        format="text"
                        label="${tool.name} k-mer abundance histogram. The
                        columns are: (1) k-mer abundance, (2) k-mer count, (3)
                        cumulative count, (4) fraction of total distinct
                        k-mers.">
                </data>
	</xml>
	<xml name="output_sequences">
                <data   name="output"
                        format="input"
                        label="${tool.name} processed nucleotide sequence file">
                        <discover_datasets pattern="__name__" directory="output" visible="true"/>
                </data>
	</xml>
	<xml name="output_sequences_single">
                <data   name="output"
                        format="input"
                        label="${tool.name} processed nucleotide sequence file" />
	</xml>
	<xml name="input_zero">
                <param  name="zero"
                        type="boolean"

	<xml name="counting-citation">
		<citation type="doi">10.1371/journal.pone.0101271</citation>
	</xml>
	<xml name="stdio">
	<stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
		<exit_code	range="1:"
				level="fatal" />
	</stdio>
	</xml>
</macros>

60:fe697e0cb24a

<macros>
	<xml name="requirements">
		<requirements>
			<requirement type="package" version="2.0rc1">khmer</requirement>
		</requirements>
	</xml>
	<xml name="version">
		<version_command>@BINARY@ --version</version_command>
	</xml>
	<token name="@TABLEPARAMS@">#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"

                        label="the k-mer counting table 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 counting table." />
	</xml>
	<xml name="abundance-histogram-output">
                <data   name="output_histogram_filename"
                        format="txt"
                        label="${tool.name} k-mer abundance histogram. The
                        columns are: (1) k-mer abundance, (2) k-mer count, (3)
                        cumulative count, (4) fraction of total distinct
                        k-mers.">
                </data>
	</xml>
	<xml name="output_sequences">
                <data   name="output"
                        format_source="inputs"
                        label="${tool.name} processed nucleotide sequence file">
                        <discover_datasets pattern="__name__" 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"

	<xml name="counting-citation">
		<citation type="doi">10.1371/journal.pone.0101271</citation>
	</xml>
	<xml name="stdio">
	<stdio>
		<exit_code	range="1:"
				level="fatal" />
	</stdio>
	</xml>
</macros>