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comparison do-partition.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-do-partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@-4">
2 <description>Load, partition, and annotate FAST[AQ] sequences</description>
3 <macros>
4 <token name="@BINARY@">do-partition.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 #for $num, $input in enumerate($inputs)
13 ln -s ${input} sequence-${num} &&
14 #end for
15 mkdir -p output && cd output &&
16 @BINARY@
17 @TABLEPARAMS@
18 @THREADS@
19 output
20 ../sequence-*
21 &&
22 mv output.info $information
23 ]]>
24 </command>
25 <inputs>
26 <expand macro="input_sequences_filenames" />
27 <expand macro="tableinputs" />
28 </inputs>
29 <outputs>
30 <data name="information" format="txt" label="${tool.name} summary." />
31 <collection name="annotated_sequence_files" type="list">
32 <discover_datasets pattern="__name__" directory="output" />
33 </collection>
34 </outputs>
35 <tests>
36 <test>
37 <param name="inputs" value="random-20-a.fa"/>
38 <output_collection name="annotated_sequence_files" type="list">
39 <element name="sequence-0.part" file="random-20-a.fa.part" />
40 </output_collection>
41 </test>
42 </tests>
43 <help><![CDATA[
44 Load in a set of sequences, partition them, merge the partitions, and
45 annotate the original sequences files with the partition information.
46
47 This script combines the functionality of `load-graph.py`,
48 `partition-graph.py`, `merge-partitions.py`, and
49 `annotate-partitions.py` into one script. This is convenient
50 but should probably not be used for large data sets, because
51 `do-partition.py` doesn't provide save/resume functionality.
52 ]]>
53 </help>
54 <citations>
55 <expand macro="software-citation" />
56 <expand macro="graph-citation" />
57 </citations>
58 </tool>