Mercurial > repos > iuc > khmer_filter_abundance

comparison filter-abund.xml @ 7:8c6433857aa8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 16:05:31 -0500
parents 03246d4ea8cd
children 97f65399e30d
comparison
equal deleted inserted replaced
6:dbe616d126b1 7:8c6433857aa8
1 <tool id="khmer_filter_abundance" name="Filter reads" version="@WRAPPER_VERSION@.0"> 1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@">
2 <description> 2 <description>
3 by minimal k-mer abundance 3 by minimal k-mer abundance
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@BINARY@">filter-abund.py</token> 6 <token name="@BINARY@">filter-abund.py</token>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version" /> 11 <expand macro="version" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 set -xu && 13 set -u &&
14 #for $num, $input in enumerate($inputs) 14 @LINK_SEQUENCES@
15 ln -s ${input} filter-abund-sequence-${num} &&
16 #end for
17 mkdir output && cd output && 15 mkdir output && cd output &&
18 @BINARY@ 16 @BINARY@
19 --cutoff=${cutoff} 17 --cutoff=${cutoff}
20 ${variable_coverage} 18 ${variable_coverage}
21 @THREADS@ 19 @THREADS@
22 ${input_countgraph_filename} 20 ${input_countgraph_filename}
23 ../filter-abund-sequence* 21 @USE_SEQUENCES@
24 ]]> 22 ]]>
25 </command> 23 </command>
26 <inputs> 24 <inputs>
27 <expand macro="input_sequences_filenames" /> 25 <expand macro="input_sequences_filenames" />
28 <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue="" 26 <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
29 label="Variable coverage" 27 label="Variable coverage"
30 help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" /> 28 help="Only trim when a sequence has high enough coverage; median abundance > 20" />
31 <param name="cutoff" type="integer" value="2" label="Cutoff" 29 <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff"
32 help="Trim at k-mers below this abundance. (--cutoff)" /> 30 help="Trim at k-mers below this abundance" />
33 <expand macro="input_countgraph_filename" /> 31 <expand macro="input_countgraph_filename" />
34 </inputs> 32 </inputs>
35 <outputs> 33 <outputs>
36 <collection name="filter-abund-sequences" type="list"> 34 <expand macro="output_sequences" extension="abundfilt"/>
37 <discover_datasets pattern="__name__" directory="output" />
38 </collection>
39 </outputs> 35 </outputs>
40 <tests> 36 <tests>
41 <test> 37 <test>
42 <param name="inputs" value="test-abund-read-2.fa" /> 38 <param name="inputs" value="test-abund-read-2.fa" />
43 <param name="input_countgraph_filename" 39 <param name="input_countgraph_filename"
44 value="test-abund-read-2.oxlicg" ftype="oxlicg" /> 40 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
45 <output_collection name="filter-abund-sequences" type="list"> 41 <output_collection name="sequences" type="list">
46 <element name="filter-abund-sequence-0.abundfilt"> 42 <element name="test-abund-read-2.fa">
47 <assert_contents> 43 <assert_contents>
48 <has_text text="GGTTGACGGGGCTCAGGG" /> 44 <has_text text="GGTTGACGGGGCTCAGGG" />
49 </assert_contents> 45 </assert_contents>
50 </element> 46 </element>
51 </output_collection> 47 </output_collection>
53 <test> 49 <test>
54 <param name="inputs" value="test-abund-read-2.fa" /> 50 <param name="inputs" value="test-abund-read-2.fa" />
55 <param name="input_countgraph_filename" 51 <param name="input_countgraph_filename"
56 value="test-abund-read-2.oxlicg" ftype="oxlicg" /> 52 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
57 <param name="cutoff" value="1" /> 53 <param name="cutoff" value="1" />
58 <output_collection name="filter-abund-sequences" type="list"> 54 <output_collection name="sequences" type="list">
59 <element name="filter-abund-sequence-0.abundfilt"> 55 <element name="test-abund-read-2.fa">
60 <assert_contents> 56 <assert_contents>
61 <has_text text="GGTTGACGGGGCTCAGGG" /> 57 <has_text text="GGTTGACGGGGCTCAGGG" />
62 </assert_contents> 58 </assert_contents>
63 </element> 59 </element>
64 </output_collection> 60 </output_collection>