Mercurial > repos > iuc > khmer_filter_abundance

comparison filter-abund.xml @ 0:71f98f6f68af 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 09:45:40 -0500
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-1:000000000000 0:71f98f6f68af
1 <tool id="khmer_filter_abundance" name="Filter k-mer" version="@WRAPPER_VERSION@.0">
2 <description>
3 by minimal abundance
4 </description>
5 <macros>
6 <token name="@BINARY@">filter-abund.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 #for $num, $input in enumerate($inputs)
15 ln -s ${input} filter-abund-sequence-${num} &&
16 #end for
17 mkdir output && cd output &&
18 @BINARY@
19 --cutoff=${cutoff}
20 ${variable_coverage}
21 @THREADS@
22 ${input_countgraph_filename}
23 ../filter-abund-sequence*
24 ]]>
25 </command>
26 <inputs>
27 <expand macro="input_sequences_filenames" />
28 <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
29 label="Variable coverage"
30 help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" />
31 <param name="cutoff" type="integer" value="2" label="Cutoff"
32 help="Trim at k-mers below this abundance. (--cutoff)" />
33 <expand macro="input_countgraph_filename" />
34 </inputs>
35 <outputs>
36 <collection name="filter-abund-sequences" type="list">
37 <discover_datasets pattern="__name__" directory="output" />
38 </collection>
39 </outputs>
40 <tests>
41 <test>
42 <param name="inputs" value="test-abund-read-2.fa" />
43 <param name="input_countgraph_filename"
44 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
45 <output_collection name="filter-abund-sequences" type="list">
46 <element name="filter-abund-sequence-0.abundfilt">
47 <assert_contents>
48 <has_text text="GGTTGACGGGGCTCAGGG" />
49 </assert_contents>
50 </element>
51 </output_collection>
52 </test>
53 <test>
54 <param name="inputs" value="test-abund-read-2.fa" />
55 <param name="input_countgraph_filename"
56 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
57 <param name="cutoff" value="1" />
58 <output_collection name="filter-abund-sequences" type="list">
59 <element name="filter-abund-sequence-0.abundfilt">
60 <assert_contents>
61 <has_text text="GGTTGACGGGGCTCAGGG" />
62 </assert_contents>
63 </element>
64 </output_collection>
65 </test>
66 </tests>
67 <help><![CDATA[
68 Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph
69
70 If the input sequences are from RNAseq or metagenome sequencing then
71 `--variable-coverage` should be used.
72
73 @HELP_FOOTER@
74 ]]>
75 </help>
76 <citations>
77 <expand macro="software-citation" />
78 <expand macro="counting-citation" />
79 </citations>
80 </tool>