Mercurial > repos > jjkoehorst > sapp

annotate circos.xml @ 35:fa736576c7ed draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
1 <tool id="DCircos" name="Circle Image Generator" version="0.1">
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
2 <description>Circos View</description>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
3 <requirements>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
4 <container type="docker">jjkoehorst/sappdocker:CIRCOS</container>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
5 </requirements>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
6 <command interpreter="docker">python3.4 /circos/circos.py '-input' '$input' -output '$output1' '$output2'</command>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
7 <inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
8 <param format="ttl" label="genome ttl file" name="input" type="data"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
9 </inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
10 <outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
11 <data format="png" label="CIRCLE: ${input.name}" name="output1"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
12 <data format="svg" label="CIRCLE: ${input.name}" name="output2"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
13 </outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
14 <help>Visualization of the RDF genome using CIRCOS. It requires a RDF genome with optionally gene prediction.
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
15 </help>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
16 <citations>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
17 <citation type="bibtex">@article{Krzywinski2009,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
18 abstract = {We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
19 author = {Krzywinski, Martin and Schein, Jacqueline and Birol, Inan\c{c} and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
20 doi = {10.1101/gr.092759.109},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
21 issn = {1549-5469},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
22 journal = {Genome research},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
23 keywords = {Animals,Chromosome Mapping,Chromosomes, Artificial, Bacterial,Chromosomes, Human, Pair 17,Chromosomes, Human, Pair 17: genetics,Chromosomes, Human, Pair 6,Chromosomes, Human, Pair 6: genetics,Contig Mapping,Dogs,Gene Dosage,Gene Dosage: genetics,Genome,Genome: genetics,Genomics,Humans,Lymphoma, Follicular,Lymphoma, Follicular: genetics,Software},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
24 month = sep,
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
25 number = {9},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
26 pages = {1639--45},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
27 pmid = {19541911},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
28 title = {{Circos: an information aesthetic for comparative genomics.}},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
29 url = {http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.abstract},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
30 volume = {19},
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
31 year = {2009}
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
32 }
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
33
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
34 </citation>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
35 </citations>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
36 </tool>