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macros.xml
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macros.xml
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<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=$parameters.tablesize_specific
#end if</token>
<token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
<xml name="tableinputs">
<conditional name="parameters">
<param name="type"
type="select"
label="Advanced Parameters"
help="ksize, n_tables, a specific tablesize" >
<option value="simple"
selected="true">
Hide
</option>
<option value="specific">
Show
</option>
</param>
<when value="simple">
<param name="tablesize"
type="select"
label="Sample Type"
display="radio">
<option value="1e9"
selected="true">
Microbial Genome
</option>
<option value="2e9">
Animal Transcriptome
</option>
<option value="4e9">
Small Animal Genome or
Low-Diversity Metagenome
</option>
<option value="16e9">
Large Animal Genome
</option>
</param>
</when>
<when value="specific">
<param name="ksize"
type="integer"
value="20"
label="ksize"
help="k-mer size to use" />
<param name="n_tables"
type="integer"
min="1"
value="4"
label="n_tables"
help="number of tables to use" />
<param name="tablesize_specific"
type="text"
label="tablesize"
help="lower bound on the tablesize to use" />
</when>
</conditional>
</xml>
<xml name="input_sequences_filenames">
<param name="inputs"
multiple="true"
type="data"
format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
label="FAST[AQ] file(s)"
help="Put in order of precedence such as longest reads first." />
</xml>
<xml name="input_sequence_filename">
<param name="input_sequence_filename"
type="data"
format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
label="FAST[AQ] file(s)" />
</xml>
<xml name="input_counting_table_filename">
<param name="input_counting_table_filename"
type="data"
format="ct"
label="the k-mer counting table to query"
help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." />
</xml>
<xml name="abundance-histogram-output">
<data name="output_histogram_filename"
format="text"
label="${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"
truevalue=""
falsevalue="--no-zero"
checked="true"
help="Output zero count bins (--no-zero)" />
</xml>
<xml name="software-citation">
<citation type="bibtex">@article{khmer2014,
author = "Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe,
Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and
Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille
and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus",
title = "The khmer software package: enabling efficient sequence
analysis",
year = "2014",
month = "04",
publisher = "Figshare",
url = "http://dx.doi.org/10.6084/m9.figshare.979190"
}</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>
<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>