Mercurial > repos > peterjc > rxlr_venn_workflow
comparison README.rst @ 8:2dfe8b788fb6 draft
Uploaded v0.0.1h, attempt to show image in README file
author | peterjc |
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date | Mon, 19 Aug 2013 13:22:30 -0400 |
parents | 51aeb3d4799d |
children | d893133128d8 |
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7:51aeb3d4799d | 8:2dfe8b788fb6 |
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13 | 13 |
14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz | 14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz |
15 | 15 |
16 You can upload this directly into Galaxy via this URL. Galaxy will handle | 16 You can upload this directly into Galaxy via this URL. Galaxy will handle |
17 removing the gzip compression to give you the FASTA protein file which | 17 removing the gzip compression to give you the FASTA protein file which |
18 has 19,805 protein sequences. Of these, only 79 sequences pass all three | 18 has 19,805 protein sequences. The expected results: |
19 of the RXLR prediction tools. | 19 |
20 * 89 RXLRs using Whisson et al. (2007) | |
21 * 124 RXLRs using Win et al. (2007) | |
22 * 162 RXLRs using Bhattacharjee et al. (006) | |
23 | |
24 Of these, only 79 sequences pass all three of the RXLR prediction tools, | |
25 while 19643 have no RXLR matches at all. | |
26 | |
27 .. image:: Phyca11_example_output.png | |
28 :height: 400px | |
29 :width: 400px | |
30 :alt: RXLR Venn diagram using Phytophthora capsici (Phyca11) | |
20 | 31 |
21 | 32 |
22 Citation | 33 Citation |
23 ======== | 34 ======== |
24 | 35 |
84 | 95 |
85 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | 96 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow |
86 | 97 |
87 To prepare the tar-ball for uploading to the Tool Shed, I use this: | 98 To prepare the tar-ball for uploading to the Tool Shed, I use this: |
88 | 99 |
89 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga | 100 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png |
90 | 101 |
91 Check this, | 102 Check this, |
92 | 103 |
93 $ tar -tzf rxlr_venn_workflow.tar.gz | 104 $ tar -tzf rxlr_venn_workflow.tar.gz |
94 README.rst | 105 README.rst |
95 repository_dependencies.xml | 106 repository_dependencies.xml |
96 rxlr_venn_workflow.ga | 107 rxlr_venn_workflow.ga |
108 Phyca11_example_output.png |