Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff

comparison filter-below-abund.xml @ 7:569001af897d 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 16:01:57 -0500
parents bf716cfc3225
children b469ab47b490
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6:bf716cfc3225 7:569001af897d
1 <tool id="khmer_filter_below_abundance_cutoff" name="Filter reads" version="@WRAPPER_VERSION@.0"> 1 <tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@">
2 <description> 2 <description>
3 below k-mer abundance of 50 3 below k-mer abundance of 50
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@BINARY@">filter-below-abund.py</token> 6 <token name="@BINARY@">filter-below-abund.py</token>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements">
10 <requirement type="package" version="1.0.1">screed</requirement>
11 </expand>
10 <expand macro="stdio" /> 12 <expand macro="stdio" />
11 <command><![CDATA[ 13 <command><![CDATA[
12 #for $num, $input in enumerate($inputs) 14 @LINK_SEQUENCES@
13 ln -s '${input}' sequence-${num} && 15 mkdir output &&
14 #end for 16 cd output &&
15 mkdir output && 17 python '$__tool_directory__/@BINARY@'
16 cd output && 18 '${input_countgraph_filename}'
17 python '$__tool_directory__/@BINARY@' 19 @USE_SEQUENCES@
18 '${input_countgraph_filename}' 20 > '$log'
19 #for $num, $input in enumerate($inputs) 21 ]]>
20 ../sequence-${num}
21 #end for
22 ]]>
23 </command> 22 </command>
24 <inputs> 23 <inputs>
25 <expand macro="input_sequences_filenames" /> 24 <expand macro="input_sequences_filenames" />
26 <expand macro="input_countgraph_filename" /> 25 <expand macro="input_countgraph_filename" />
27 </inputs> 26 </inputs>
28 <outputs> 27 <outputs>
29 <collection name="sequence_files" type="list"> 28 <data name="log" format="txt" />
30 <discover_datasets pattern="__name__" directory="output" /> 29 <expand macro="output_sequences" extension="below"/>
31 </collection>
32 </outputs> 30 </outputs>
33 <tests> 31 <tests>
34 <test> 32 <test>
35 <param name="inputs" value="test-abund-read-2.fa" /> 33 <param name="inputs" value="test-abund-read-2.fa" />
36 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" /> 34 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
37 <output_collection name="sequence_files"> 35 <output_collection name="sequences">
38 <element name="sequence-0.below" file="test-abund-read-2.fa.below" /> 36 <element name="test-abund-read-2.fa" file="test-abund-read-2.fa.below" />
39 </output_collection> 37 </output_collection>
40 </test> 38 </test>
41 </tests> 39 </tests>
42 <help><![CDATA[ 40 <help><![CDATA[
43 Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. 41 Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph.