Mercurial > repos > iuc > khmer_partition

annotate do-partition.xml @ 7:b7429b53be2a 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/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
author iuc
date Tue, 23 Mar 2021 21:30:35 +0000
parents e562293ee5ec
children 5a0fa29951ae
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
b7429b53be2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 6
diff changeset
1 <tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
2 <description>Load, partition, and annotate sequences</description>
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
3 <macros>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
4 <token name="@BINARY@">do-partition.py</token>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
5 <import>macros.xml</import>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
6 </macros>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
7 <expand macro="requirements" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
8 <expand macro="stdio" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
9 <expand macro="version" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
10 <command><![CDATA[
6
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
11 set -u &&
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
12 @LINK_SEQUENCES@
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
13 mkdir -p output && cd output &&
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
14 @BINARY@
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
15 @TABLEPARAMS@
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
16 @THREADS@
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
17 output
6
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
18 @USE_SEQUENCES@
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
19 ]]>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
20 </command>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
21 <inputs>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
22 <expand macro="input_sequences_filenames" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
23 <expand macro="tableinputs" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
24 </inputs>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
25 <outputs>
6
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
26 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} on ${on_string}: summary." />
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
27 <expand macro="output_sequences" extension="part"/>
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
28 </outputs>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
29 <tests>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
30 <test>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
31 <param name="inputs" value="random-20-a.fa"/>
6
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
32 <output_collection name="sequences" type="list">
e562293ee5ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 2
diff changeset
33 <element name="random-20-a.fa" file="random-20-a.fa.part" />
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
34 </output_collection>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
35 </test>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
36 </tests>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
37 <help><![CDATA[
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
38 Load in a set of sequences, partition them, merge the partitions, and
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
39 annotate the original sequences files with the partition information.
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
40
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
41 This script combines the functionality of `load-graph.py`,
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
42 `partition-graph.py`, `merge-partitions.py`, and
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
43 `annotate-partitions.py` into one script. This is convenient
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
44 but should probably not be used for large data sets, because
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
45 `do-partition.py` doesn't provide save/resume functionality.
2
09779cc94f94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
parents: 0
diff changeset
46
0
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
47 ]]>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
48 </help>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
49 <citations>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
50 <expand macro="software-citation" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
51 <expand macro="graph-citation" />
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
52 </citations>
1413823dce99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff changeset
53 </tool>