Mercurial > repos > iuc > khmer_abundance_distribution_single
diff abundance-dist-single.xml @ 0:47cea67b74ea draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author | iuc |
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date | Wed, 11 Nov 2015 09:47:17 -0500 |
parents | |
children | a3a5a1e44d18 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance-dist-single.xml Wed Nov 11 09:47:17 2015 -0500 @@ -0,0 +1,91 @@ +<tool id="khmer_abundance_distribution_single" name="Abundance Distribution (all-in-one)" version="@WRAPPER_VERSION@.0"> + <description> + Calculate abundance distribution of the k-mers in a given sequence file + </description> + <macros> + <token name="@BINARY@">abundance-dist-single.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version" /> + <command><![CDATA[ +set -xu && +mkdir output && cd output && +@BINARY@ +@TABLEPARAMS@ +${zero} +${bigcount} +#if $save_countgraph + --savegraph=${optional_output_countgraph} +#end if +--squash +@THREADS@ +${input_sequence_filename} +${output_histogram_filename} + +]]> + </command> + <inputs> + <expand macro="input_sequence_filename" /> + <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file" + help="(--savegraph)" /> + <expand macro="input_zero" /> + <expand macro="input_bigcount" /> + <expand macro="tableinputs" /> + </inputs> + <outputs> + <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} k-mer countgraph"> + <filter>save_countgraph == True</filter> + </data> + <expand macro="abundance-histogram-output" /> + </outputs> + <tests> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="type" value="specific" /> + <param name="tablesize_specific" value="1e7" /> + <param name="n_tables" value="2" /> + <param name="ksize" value="17" /> + <param name="no_zero" value="false" /> + <output name="output_histogram_filename" ftpye="txt"> + <assert_contents> + <has_text text="1,96,96,0.98" /> + <has_text text="1001,2,98,1.0" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="type" value="specific" /> + <param name="tablesize_specific" value="1e7" /> + <param name="n_tables" value="2" /> + <param name="ksize" value="17" /> + <param name="no_zero" value="false" /> + <param name="bigcount" value="false" /> + <output name="output_histogram_filename" ftype="txt"> + <assert_contents> + <has_text text="1,96,96,0.98" /> + <has_text text="255,2,98,1.0" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +Calculate the abundance distribution of k-mers from a single sequence file. + +Note that with `-b` this script is constant memory; in exchange, +k-mer counts will stop at 255. The memory usage of this script with +`-b` will be about 1.15x the product of the `-x` and +`-N` numbers. + + +@HELP_FOOTER@ +]]> + </help> + <citations> + <expand macro="software-citation" /> + <expand macro="counting-citation" /> + </citations> +</tool>