Mercurial > repos > iuc > khmer_abundance_distribution_single

comparison abundance-dist-single.xml @ 10:65b382bf9b7c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:47:14 +0000
parents 385a965c6f87
children
comparison
equal deleted inserted replaced
9:385a965c6f87 10:65b382bf9b7c
1 <tool id="khmer_abundance_distribution_single" name="khmer: Abundance Distribution (all-in-one)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="khmer_abundance_distribution_single" name="khmer: Abundance Distribution (all-in-one)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Calculate abundance distribution of k-mers 3 Calculate abundance distribution of k-mers
4 </description> 4 </description>
5 <expand macro="bio_tools"/>
6 <macros> 5 <macros>
7 <token name="@BINARY@">abundance-dist-single.py</token> 6 <token name="@BINARY@">abundance-dist-single.py</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
9 <expand macro="bio_tools"/>
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <expand macro="version" /> 12 <expand macro="version" />
13 <command><![CDATA[ 13 <command><![CDATA[
14 set -u && 14 set -u &&
33 <expand macro="input_zero" /> 33 <expand macro="input_zero" />
34 <expand macro="input_bigcount" /> 34 <expand macro="input_bigcount" />
35 <expand macro="tableinputs" /> 35 <expand macro="tableinputs" />
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>
38 <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} on ${on_string} k-mer countgraph"> 38 <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
39 <filter>save_countgraph == True</filter> 39 <filter>save_countgraph == True</filter>
40 </data> 40 </data>
41 <expand macro="abundance-histogram-output" /> 41 <expand macro="abundance-histogram-output" />
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test> 44 <test expect_num_outputs="1">
45 <param name="input_sequence_filename" value="test-abund-read-2.fa" /> 45 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
46 <param name="type" value="specific" /> 46 <param name="type" value="specific" />
47 <param name="tablesize_specific" value="1e7" /> 47 <param name="tablesize_specific" value="1e7" />
48 <param name="n_tables" value="2" /> 48 <param name="n_tables" value="2" />
49 <param name="ksize" value="17" /> 49 <param name="ksize" value="17" />
50 <param name="no_zero" value="false" /> 50 <param name="no_zero" value="false" />
51 <output name="output_histogram_filename" ftype="txt"> 51 <output name="output_histogram_filename" ftype="csv">
52 <assert_contents> 52 <assert_contents>
53 <has_text text="1,96,96,0.98" /> 53 <has_text text="1,96,96,0.98" />
54 <has_text text="1001,2,98,1.0" /> 54 <has_text text="1001,2,98,1.0" />
55 </assert_contents> 55 </assert_contents>
56 </output> 56 </output>
57 </test> 57 </test>
58 <test> 58 <test expect_num_outputs="2">
59 <param name="input_sequence_filename" value="test-abund-read-2.fq.gz" /> 59 <param name="input_sequence_filename" value="test-abund-read-2.fq.gz" />
60 <param name="type" value="specific" /> 60 <param name="type" value="specific" />
61 <param name="tablesize_specific" value="1e7" /> 61 <param name="tablesize_specific" value="1e7" />
62 <param name="n_tables" value="2" /> 62 <param name="n_tables" value="2" />
63 <param name="ksize" value="17" /> 63 <param name="ksize" value="17" />
64 <param name="no_zero" value="false" /> 64 <param name="no_zero" value="false" />
65 <param name="bigcount" value="false" /> 65 <param name="bigcount" value="false" />
66 <output name="output_histogram_filename" ftype="txt"> 66 <param name="save_countgraph" value="true"/>
67 <output name="output_histogram_filename" ftype="csv">
67 <assert_contents> 68 <assert_contents>
68 <has_text text="1,96,96,0.98" /> 69 <has_text text="1,96,96,0.98" />
69 <has_text text="255,2,98,1.0" /> 70 <has_text text="255,2,98,1.0" />
71 </assert_contents>
72 </output>
73 <output name="optional_output_countgraph">
74 <assert_contents>
75 <has_size size="1k"/>
70 </assert_contents> 76 </assert_contents>
71 </output> 77 </output>
72 </test> 78 </test>
73 79
74 </tests> 80 </tests>
78 Note that with `-b` this script is constant memory; in exchange, 84 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 85 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 86 `-b` will be about 1.15x the product of the `-x` and
81 `-N` numbers. 87 `-N` numbers.
82 88
89 @ABUNDANCE_HISTOGRAM_OUTPUT_HELP@
83 90
84 @HELP_FOOTER@ 91 @HELP_FOOTER@
85 ]]> 92 ]]>
86 </help> 93 </help>
87 <citations> 94 <citations>