Mercurial > repos > iuc > khmer_partition
view macros.xml @ 7:b7429b53be2a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
author | iuc |
---|---|
date | Tue, 23 Mar 2021 21:30:35 +0000 |
parents | e562293ee5ec |
children | 5a0fa29951ae |
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<macros> <token name="@TOOL_VERSION@">3.0.0a3</token> <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">khmer</requirement> <yield/> </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 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> <token name="@LINK_SEQUENCES@"> <![CDATA[ #import re mkdir input/ && #set gzip="" #for $num, $input in enumerate($inputs) ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' && #if str($input).endswith(".gz"): #set gzip="--gzip" #end if #end for]]></token> <token name="@USE_SEQUENCES@"> <![CDATA[ #for $num, $input in enumerate($inputs) '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' #end for]]></token> <xml name="input_sequences_filenames"> <param name="inputs" multiple="true" type="data" format="fasta,fastq,fasta.gz,fastq.gz" 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,fasta.gz,fastq.gz" 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} on ${on_string}: k-mer abundance histogram. The columns are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers." /> </xml> <xml name="output_sequences" token_extension=""> <collection name="sequences" type="list"> <discover_datasets pattern="(?P<name>.*)\.(?P<ext>fast[aq](\.gz)?)\.@EXTENSION@" directory="output" /> </collection> </xml> <xml name="output_sequences_single"> <data name="output" format_source="input_sequence_filename" label="${tool.name} on ${on_string}: processed nucleotide sequence file" /> </xml> <xml name="input_zero"> <param argument="--no-zero" name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true" help="Output zero count bins" /> </xml> <xml name="input_bigcount"> <param argument="--no-bigcount" name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount" checked="true" help="Count k-mers past 255 occurences" /> </xml> <token name="@HELP_FOOTER@"><![CDATA[ (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token> <xml name="software-citation"> <citation type="doi">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="doi">10.1073/pnas.1121464109</citation> </xml> <xml name="counting-citation"> <citation type="doi">10.1371/journal.pone.0101271</citation> </xml> </macros>