Mercurial > repos > iuc > khmer_partition

annotate do-partition.xml @ 4:c72a41a26c7d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
author iuc
date Wed, 09 Nov 2016 06:05:04 -0500
parents 69180013f797
children de6ba32d6021
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
1 <tool id="khmer_partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@.0">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
2 <description>Load, partition, and annotate FAST[AQ] sequences</description>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
3 <macros>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
4 <token name="@BINARY@">do-partition.py</token>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
5 <import>macros.xml</import>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
6 </macros>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
7 <expand macro="requirements" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
8 <expand macro="stdio" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
9 <expand macro="version" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
10 <command><![CDATA[
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
11 set -xu &&
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
12 #for $num, $input in enumerate($inputs)
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
13 ln -s ${input} sequence-${num} &&
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
14 #end for
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
15 mkdir -p output && cd output &&
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
16 @BINARY@
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
17 @TABLEPARAMS@
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
18 @THREADS@
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
19 output
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
20 ../sequence-*
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
21 ]]>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
22 </command>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
23 <inputs>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
24 <expand macro="input_sequences_filenames" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
25 <expand macro="tableinputs" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
26 </inputs>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
27 <outputs>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
28 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} summary." />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
29 <collection name="annotated_sequence_files" type="list">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
30 <discover_datasets pattern="__name__" directory="output" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
31 </collection>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
32 </outputs>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
33 <tests>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
34 <test>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
35 <param name="inputs" value="random-20-a.fa"/>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
36 <output_collection name="annotated_sequence_files" type="list">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
37 <element name="sequence-0.part" file="random-20-a.fa.part" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
38 </output_collection>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
39 </test>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
40 </tests>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
41 <help><![CDATA[
4
c72a41a26c7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
parents: 0
diff changeset
42
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
43 Load in a set of sequences, partition them, merge the partitions, and
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
44 annotate the original sequences files with the partition information.
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
45
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
46 This script combines the functionality of `load-graph.py`,
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
47 `partition-graph.py`, `merge-partitions.py`, and
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
48 `annotate-partitions.py` into one script. This is convenient
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
49 but should probably not be used for large data sets, because
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
50 `do-partition.py` doesn't provide save/resume functionality.
4
c72a41a26c7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
parents: 0
diff changeset
51
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
52 ]]>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
53 </help>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
54 <citations>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
55 <expand macro="software-citation" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
56 <expand macro="graph-citation" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
57 </citations>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
58 </tool>