Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
changeset 10:00f7064c564b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author | iuc |
---|---|
date | Thu, 03 Oct 2024 13:46:21 +0000 |
parents | 19607c740d19 |
children | |
files | filter-below-abund.xml macros.xml |
diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/filter-below-abund.xml Mon Jun 17 11:47:14 2024 +0000 +++ b/filter-below-abund.xml Thu Oct 03 13:46:21 2024 +0000 @@ -2,11 +2,11 @@ <description> below k-mer abundance of 50 </description> - <expand macro="bio_tools"/> <macros> <token name="@BINARY@">filter-below-abund.py</token> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"> <requirement type="package" version="1.0.1">screed</requirement> </expand> @@ -18,7 +18,6 @@ python '$__tool_directory__/@BINARY@' '${input_countgraph_filename}' @USE_SEQUENCES@ -> '$log' ]]> </command> <inputs> @@ -26,7 +25,6 @@ <expand macro="input_countgraph_filename" /> </inputs> <outputs> - <data name="log" format="txt" /> <expand macro="output_sequences" extension="below"/> </outputs> <tests>
--- a/macros.xml Mon Jun 17 11:47:14 2024 +0000 +++ b/macros.xml Thu Oct 03 13:46:21 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.0.0a3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.01</token> <xml name="bio_tools"> <xrefs> @@ -34,7 +34,7 @@ #end if ]]> </token> - <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> + <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token> <xml name="tableinputs"> <conditional name="parameters"> <param name="type" type="select" label="Advanced Parameters" @@ -43,7 +43,7 @@ <option value="specific">Show</option> </param> <when value="simple"> - <param argument="" name="tablesize" type="select" label="Sample Type" display="radio"> + <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> @@ -51,8 +51,8 @@ </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="--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> @@ -90,11 +90,13 @@ 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 ${on_string}: k-mer abundance histogram. The - columns are: (1) k-mer abundance, (2) k-mer count, (3) - cumulative count, (4) fraction of total distinct k-mers." /> + <data name="output_histogram_filename" format="csv" + label="${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<name>.*)\.(?P<ext>fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />