Mercurial > repos > iuc > khmer_partition

comparison do-partition.xml @ 8:de6ba32d6021 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 20:57:16 +0000
parents c72a41a26c7d
children 94e459e086bb
comparison
equal deleted inserted replaced
7:3f0d5322fe37 8:de6ba32d6021
1 <tool id="khmer_partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@.0"> 1 <tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@WRAPPER_VERSION@@TOOL_VERSION@">
2 <description>Load, partition, and annotate FAST[AQ] sequences</description> 2 <description>Load, partition, and annotate sequences</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">do-partition.py</token> 4 <token name="@BINARY@">do-partition.py</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version" /> 9 <expand macro="version" />
10 <command><![CDATA[ 10 <command><![CDATA[
11 set -xu && 11 set -u &&
12 #for $num, $input in enumerate($inputs) 12 @LINK_SEQUENCES@
13 ln -s ${input} sequence-${num} &&
14 #end for
15 mkdir -p output && cd output && 13 mkdir -p output && cd output &&
16 @BINARY@ 14 @BINARY@
17 @TABLEPARAMS@ 15 @TABLEPARAMS@
18 @THREADS@ 16 @THREADS@
19 output 17 output
20 ../sequence-* 18 @USE_SEQUENCES@
21 ]]> 19 ]]>
22 </command> 20 </command>
23 <inputs> 21 <inputs>
24 <expand macro="input_sequences_filenames" /> 22 <expand macro="input_sequences_filenames" />
25 <expand macro="tableinputs" /> 23 <expand macro="tableinputs" />
26 </inputs> 24 </inputs>
27 <outputs> 25 <outputs>
28 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} summary." /> 26 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} on ${on_string}: summary." />
29 <collection name="annotated_sequence_files" type="list"> 27 <expand macro="output_sequences" extension="part"/>
30 <discover_datasets pattern="__name__" directory="output" />
31 </collection>
32 </outputs> 28 </outputs>
33 <tests> 29 <tests>
34 <test> 30 <test>
35 <param name="inputs" value="random-20-a.fa"/> 31 <param name="inputs" value="random-20-a.fa"/>
36 <output_collection name="annotated_sequence_files" type="list"> 32 <output_collection name="sequences" type="list">
37 <element name="sequence-0.part" file="random-20-a.fa.part" /> 33 <element name="random-20-a.fa" file="random-20-a.fa.part" />
38 </output_collection> 34 </output_collection>
39 </test> 35 </test>
40 </tests> 36 </tests>
41 <help><![CDATA[ 37 <help><![CDATA[
42
43 Load in a set of sequences, partition them, merge the partitions, and 38 Load in a set of sequences, partition them, merge the partitions, and
44 annotate the original sequences files with the partition information. 39 annotate the original sequences files with the partition information.
45 40
46 This script combines the functionality of `load-graph.py`, 41 This script combines the functionality of `load-graph.py`,
47 `partition-graph.py`, `merge-partitions.py`, and 42 `partition-graph.py`, `merge-partitions.py`, and