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comparison filter-below-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-below-abund" name="Filter below abundance cutoff of 50" version="@WRAPPER_VERSION@-3">
2 <description>
3 Trims fastq/fasta sequences at k-mers with abundance below 50
4 based on a provided k-mer countgraph
5 </description>
6 <macros>
7 <token name="@BINARY@">filter-below-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 ${input} sequence-${num} &&
17 mkdir output && cd output &&
18 @BINARY@
19 ${input_countgraph_filename}
20 ../sequence*
21 ]]>
22 </command>
23 <inputs>
24 <expand macro="input_sequences_filenames" />
25 <expand macro="input_countgraph_filename" />
26 </inputs>
27 <outputs>
28 <collection name="sequence_files" type="list">
29 <discover_datasets pattern="__name__" directory="output" />
30 </collection>
31 </outputs>
32 <tests>
33 <test>
34 <param name="inputs" value="test-abund-read-2.fa" />
35 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
36 <output_collection name="sequence_files">
37 <element name="sequence-0.below" file="test-abund-read-2.fa.below" />
38 </output_collection>
39 </test>
40 </tests>
41 <help><![CDATA[
42 Trims sequences at the first kmer with abundance above 50.
43
44 @HELP_FOOTER@
45 ]]></help>
46 <citations>
47 <expand macro="software-citation" />
48 <expand macro="counting-citation" />
49 </citations>
50 </tool>