Mercurial > repos > iuc > khmer_filter_abundance
comparison filter-abund.xml @ 0:71f98f6f68af draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author | iuc |
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date | Wed, 11 Nov 2015 09:45:40 -0500 |
parents | |
children | 03246d4ea8cd |
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-1:000000000000 | 0:71f98f6f68af |
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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> |