Mercurial > repos > iuc > bandage

annotate macros.xml @ 5:0d1b07907bb1 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/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Mon, 30 Aug 2021 21:45:02 +0000
parents 97f832fc1267
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
1 <macros>
2
42348f95138d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
iuc
parents: 1
diff changeset
2 <token name="@TOOL_VERSION@">0.8.1</token>
0
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
3 <xml name="requirements">
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
4 <requirements>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">bandage</requirement>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
6 </requirements>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
7 </xml>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
8 <xml name="version_command">
3
97f832fc1267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit ef940ee99e8bf07cfe86b273a3eda72f09003fb3"
iuc
parents: 2
diff changeset
9 <version_command>@HEADLESS@ Bandage --version</version_command>
0
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
10 </xml>
5
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
11 <xml name="bio_tools">
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
12 <xrefs>
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
13 <xref type="bio.tools">bandage</xref>
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
14 </xrefs>
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
15 </xml>
0d1b07907bb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
16 <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token>
0
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
17 <token name="@BANDAGE_OVERVIEW@">
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
18
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
19 **Bandage Overview**
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
20
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
21 Bandage is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others.
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
22 De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone.
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
23
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
24 Bandage works with Graphical Fragment Assembly (GFA) files. For more information about this file format, see here_
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
25
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
26 .. _here: https://gfa-spec.github.io/GFA-spec/GFA2.html
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
27 </token>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
28 <xml name="citations">
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
29 <citations>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
30 <citation type="doi">10.1093/bioinformatics/btv383</citation>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
31 </citations>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
32 </xml>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
parents:
diff changeset
33 </macros>