Mercurial > repos > iuc > khmer_abundance_distribution_single

comparison abundance-dist-single.xml @ 0:47cea67b74ea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:47:17 -0500
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1 <tool id="khmer_abundance_distribution_single" name="Abundance Distribution (all-in-one)" version="@WRAPPER_VERSION@.0">
2 <description>
3 Calculate abundance distribution of the k-mers in a given sequence file
4 </description>
5 <macros>
6 <token name="@BINARY@">abundance-dist-single.py</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version" />
12 <command><![CDATA[
13 set -xu &&
14 mkdir output && cd output &&
15 @BINARY@
16 @TABLEPARAMS@
17 ${zero}
18 ${bigcount}
19 #if $save_countgraph
20 --savegraph=${optional_output_countgraph}
21 #end if
22 --squash
23 @THREADS@
24 ${input_sequence_filename}
25 ${output_histogram_filename}
26
27 ]]>
28 </command>
29 <inputs>
30 <expand macro="input_sequence_filename" />
31 <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file"
32 help="(--savegraph)" />
33 <expand macro="input_zero" />
34 <expand macro="input_bigcount" />
35 <expand macro="tableinputs" />
36 </inputs>
37 <outputs>
38 <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
39 <filter>save_countgraph == True</filter>
40 </data>
41 <expand macro="abundance-histogram-output" />
42 </outputs>
43 <tests>
44 <test>
45 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
46 <param name="type" value="specific" />
47 <param name="tablesize_specific" value="1e7" />
48 <param name="n_tables" value="2" />
49 <param name="ksize" value="17" />
50 <param name="no_zero" value="false" />
51 <output name="output_histogram_filename" ftpye="txt">
52 <assert_contents>
53 <has_text text="1,96,96,0.98" />
54 <has_text text="1001,2,98,1.0" />
55 </assert_contents>
56 </output>
57 </test>
58 <test>
59 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
60 <param name="type" value="specific" />
61 <param name="tablesize_specific" value="1e7" />
62 <param name="n_tables" value="2" />
63 <param name="ksize" value="17" />
64 <param name="no_zero" value="false" />
65 <param name="bigcount" value="false" />
66 <output name="output_histogram_filename" ftype="txt">
67 <assert_contents>
68 <has_text text="1,96,96,0.98" />
69 <has_text text="255,2,98,1.0" />
70 </assert_contents>
71 </output>
72 </test>
73
74 </tests>
75 <help><![CDATA[
76 Calculate the abundance distribution of k-mers from a single sequence file.
77
78 Note that with `-b` this script is constant memory; in exchange,
79 k-mer counts will stop at 255. The memory usage of this script with
80 `-b` will be about 1.15x the product of the `-x` and
81 `-N` numbers.
82
83
84 @HELP_FOOTER@
85 ]]>
86 </help>
87 <citations>
88 <expand macro="software-citation" />
89 <expand macro="counting-citation" />
90 </citations>
91 </tool>