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comparison extract-partitions.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-extract-partitions" name="Extract partitions" version="@WRAPPER_VERSION@-2">
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 set -xu &&
12 mkdir -p output &&
13 cd output &&
14 @BINARY@
15 --max-size $max_size
16 --min-partition-size $min_partition_size
17 $output_unassigned
18 output
19 #for input in $inputs
20 $input
21 #end for
22 &&
23 mv output.dist $distribution
24 ]]>
25 </command>
26 <inputs>
27 <expand macro="input_sequences_filenames" />
28 <param name="max_size" type="integer" label="Max group size" value="1000000"
29 help="No more than this many number of sequences will be stored in each output (--max-size/-X)"/>
30 <param name="min_partition_size" type="integer" label="Min partition size" value="5"
31 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
32 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
33 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
34 </inputs>
35 <outputs>
36 <data name="distribution" format="txt" label="Partition size distribution from ${tool.name}" />
37 <collection name="groups-of-partitions" type="list">
38 <discover_datasets pattern="__name__" directory="output" />
39 </collection>
40 </outputs>
41 <tests>
42 <test>
43 <param name="inputs" value="random-20-a.fa.part"/>
44 <output_collection name="groups-of-partitions">
45 <element name="output.group0000.part" file="random-20-a.part.extract.fa" />
46 </output_collection>
47 </test>
48
49 </tests>
50 <help><![CDATA[
51 Separate sequences that are annotated with partitions into grouped files.
52
53 @HELP_FOOTER@
54 ]]>
55 </help>
56 <citations>
57 <expand macro="software-citation" />
58 <expand macro="graph-citation" />
59 </citations>
60 </tool>