Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
comparison filter-below-abund.xml @ 0:67b597ec0baf 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 09:46:57 -0500 |
parents | |
children | e0e33e40d7c4 |
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-1:000000000000 | 0:67b597ec0baf |
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1 <tool id="khmer_filter_below_abundance_cutoff" name="Filter k-mers" version="@WRAPPER_VERSION@.0"> | |
2 <description> | |
3 below abundance cutoff of 50 | |
4 </description> | |
5 <macros> | |
6 <token name="@BINARY@">filter-below-abund.py</token> | |
7 <import>macros.xml</import> | |
8 </macros> | |
9 <expand macro="requirements" /> | |
10 <expand macro="stdio" /> | |
11 <command><![CDATA[ | |
12 #for $num, $input in enumerate($inputs) | |
13 ln -s ${input} sequence-${num} && | |
14 #end for | |
15 mkdir output && | |
16 cd output && | |
17 $__tool_directory__/@BINARY@ | |
18 ${input_countgraph_filename} | |
19 #for $num, $input in enumerate($inputs) | |
20 ../sequence-${num} | |
21 #end for | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <expand macro="input_sequences_filenames" /> | |
26 <expand macro="input_countgraph_filename" /> | |
27 </inputs> | |
28 <outputs> | |
29 <collection name="sequence_files" type="list"> | |
30 <discover_datasets pattern="__name__" directory="output" /> | |
31 </collection> | |
32 </outputs> | |
33 <tests> | |
34 <test> | |
35 <param name="inputs" value="test-abund-read-2.fa" /> | |
36 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" /> | |
37 <output_collection name="sequence_files"> | |
38 <element name="sequence-0.below" file="test-abund-read-2.fa.below" /> | |
39 </output_collection> | |
40 </test> | |
41 </tests> | |
42 <help><![CDATA[ | |
43 Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. | |
44 | |
45 @HELP_FOOTER@ | |
46 ]]></help> | |
47 <citations> | |
48 <expand macro="software-citation" /> | |
49 <expand macro="counting-citation" /> | |
50 </citations> | |
51 </tool> |