Mercurial > repos > iuc > khmer_extract_partitions

comparison extract-partitions.xml @ 0:d5a18dd63529 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:47:38 -0500
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-1:000000000000 0:d5a18dd63529
1 <tool id="khmer_extract_partitions" name="Extract partitions" version="@WRAPPER_VERSION@.0">
2 <description>Separate sequences that are annotated with partitions into grouped files</description>
3 <macros>
4 <token name="@BINARY@">extract-partitions.py</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version" />
10 <command><![CDATA[
11 mkdir -p output &&
12 cd output &&
13 @BINARY@
14 --max-size $max_size
15 --min-partition-size $min_partition_size
16 $output_unassigned
17 output
18 #for input in $inputs
19 $input
20 #end for
21 ]]>
22 </command>
23 <inputs>
24 <expand macro="input_sequences_filenames" />
25 <param name="max_size" type="integer" label="Max group size" value="1000000"
26 help="No more than this many number of sequences will be stored in each output (--max-size/-X)"/>
27 <param name="min_partition_size" type="integer" label="Min partition size" value="5"
28 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
29 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
30 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
31 </inputs>
32 <outputs>
33 <data name="distribution" format="txt" from_work_dir="output.dist" label="Partition size distribution from ${tool.name}" />
34 <collection name="groups-of-partitions" type="list">
35 <discover_datasets pattern="__name__" directory="output" />
36 </collection>
37 </outputs>
38 <tests>
39 <test>
40 <param name="inputs" value="random-20-a.fa.part"/>
41 <output_collection name="groups-of-partitions">
42 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
43 </output_collection>
44 </test>
45
46 </tests>
47 <help><![CDATA[
48 Separate sequences that are annotated with partitions into grouped files.
49
50 @HELP_FOOTER@
51 ]]>
52 </help>
53 <citations>
54 <expand macro="software-citation" />
55 <expand macro="graph-citation" />
56 </citations>
57 </tool>