Mercurial > repos > iuc > khmer_abundance_distribution

comparison abundance-dist.xml @ 0:c07433531fd3 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 09:46:38 -0500
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children be929aa4e152
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-1:000000000000 0:c07433531fd3
1 <tool id="khmer_abundance_distribution" name="Abundance Distribution" version="@WRAPPER_VERSION@.0">
2 <description>
3 Calculate abundance distribution of the k-mers in a given sequence file using a pre-made k-mer countgraph
4 </description>
5 <macros>
6 <token name="@BINARY@">abundance-dist.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 --squash
17 ${zero}
18 ${bigcount}
19 ${input_countgraph_filename}
20 ${input_sequence_filename}
21 ${output_histogram_filename}
22 ]]>
23 </command>
24 <inputs>
25 <expand macro="input_countgraph_filename" />
26 <expand macro="input_sequence_filename" />
27 <expand macro="input_zero" />
28 <expand macro="input_bigcount" />
29 </inputs>
30 <outputs>
31 <expand macro="abundance-histogram-output" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
36 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
37 <param name="zero" value="false" />
38 <output name="output_histogram_filename">
39 <assert_contents>
40 <has_text text="1,96,96,0.98" />
41 <has_text text="1001,2,98,1.0" />
42 </assert_contents>
43 </output>
44 </test>
45 <test>
46 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
47 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
48 <param name="zero" value="false" />
49 <param name="bigcount" value="false" />
50 <output name="output_histogram_filename">
51 <assert_contents>
52 <has_text text="1,96,96,0.98" />
53 <has_text text="255,2,98,1.0" />
54 </assert_contents>
55 </output>
56 </test>
57 </tests>
58 <help><![CDATA[
59 Calculate abundance distribution of the k-mers in the sequence file using a
60 pre-made k-mer countgraph.
61
62 @HELP_FOOTER@
63 ]]>
64 </help>
65 <citations>
66 <expand macro="software-citation" />
67 <expand macro="counting-citation" />
68 </citations>
69 </tool>