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comparison filter-abund.xml @ 0:0187f18785a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author iuc
date Sat, 17 Oct 2015 04:02:33 -0400
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-1:000000000000 0:0187f18785a3
1 <tool id="gedlab-khmer-filter-abund" name="Filter by abundance" version="@WRAPPER_VERSION@-5">
2 <description>
3 Trims fastq/fasta sequences at k-mers of a given abundance
4 based on a provided k-mer countgraph
5 </description>
6 <macros>
7 <token name="@BINARY@">filter-abund.py</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="requirements" />
11 <expand macro="stdio" />
12 <expand macro="version" />
13 <command><![CDATA[
14 set -xu &&
15 #for $num, $input in enumerate($inputs)
16 ln -s ${input} filter-abund-sequence-${num} &&
17 #end for
18 mkdir output && cd output &&
19 @BINARY@
20 --cutoff=${cutoff}
21 ${variable_coverage}
22 @THREADS@
23 ${input_countgraph_filename}
24 ../filter-abund-sequence*
25 ]]>
26 </command>
27 <inputs>
28 <expand macro="input_sequences_filenames" />
29 <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
30 label="Variable coverage"
31 help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" />
32 <param name="cutoff" type="integer" value="2" label="Cutoff"
33 help="Trim at k-mers below this abundance. (--cutoff)" />
34 <expand macro="input_countgraph_filename" />
35 </inputs>
36 <outputs>
37 <collection name="filter-abund-sequences" type="list">
38 <discover_datasets pattern="__name__" directory="output" />
39 </collection>
40 </outputs>
41 <tests>
42 <test>
43 <param name="inputs" value="test-abund-read-2.fa" />
44 <param name="input_countgraph_filename"
45 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
46 <output_collection name="filter-abund-sequences" type="list">
47 <element name="filter-abund-sequence-0.abundfilt">
48 <assert_contents>
49 <has_text text="GGTTGACGGGGCTCAGGG" />
50 </assert_contents>
51 </element>
52 </output_collection>
53 </test>
54 <test>
55 <param name="inputs" value="test-abund-read-2.fa" />
56 <param name="input_countgraph_filename"
57 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
58 <param name="cutoff" value="1" />
59 <output_collection name="filter-abund-sequences" type="list">
60 <element name="filter-abund-sequence-0.abundfilt">
61 <assert_contents>
62 <has_text text="GGTTGACGGGGCTCAGGG" />
63 </assert_contents>
64 </element>
65 </output_collection>
66 </test>
67 </tests>
68 <help><![CDATA[
69 Trim sequences at a minimum k-mer abundance.
70
71 If the input sequences are from RNAseq or metagenome sequencing then
72 `--variable-coverage` should be used.
73
74 @HELP_FOOTER@
75 ]]>
76 </help>
77 <citations>
78 <expand macro="software-citation" />
79 <expand macro="counting-citation" />
80 </citations>
81 </tool>