Mercurial > repos > peterjc > blast_top_hit_species
changeset 4:7d768ff419c0 draft default tip
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
| author | peterjc |
|---|---|
| date | Wed, 09 Sep 2020 15:13:58 +0000 |
| parents | a66c358bfbcf |
| children | |
| files | README.rst repository_dependencies.xml |
| diffstat | 2 files changed, 23 insertions(+), 16 deletions(-) [+] |
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--- a/README.rst Wed Apr 08 06:06:30 2015 -0400 +++ b/README.rst Wed Sep 09 15:13:58 2020 +0000 @@ -15,7 +15,7 @@ see https://github.com/peterjc/galaxy_blast -Galaxy workflow for counting species of top BLAST hits +Galaxy workflow for counting species of top BLAST hits ====================================================== This Galaxy workflow (file ``blast_top_hit_species.ga``) is intended for an @@ -42,7 +42,8 @@ 7. Count the BLAST species names in this file. 8. Sort the counts. -Finally we would suggest visualising the sorted tally table as a Pie Chart. +Finally we would suggest visualising the sorted tally table as a Pie Chart, +as in the example below. Sample Data @@ -50,7 +51,7 @@ As an example, you can upload the transcriptome assembly of the nematode *Nacobbus abberans* from Eves van den Akker *et al.* (2015), -http://dx.doi.org/10.1093/gbe/evu171 using this URL: +https://doi.org/10.1093/gbe/evu171 using this URL: http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_reference_no_contam.zip @@ -72,7 +73,7 @@ ... ... ===== ================== -As you might guess from the filename ``N.abberans_reference_no_contam.fasta``, +As you might guess from the filename ``N.abberans_reference_no_contam.fasta``, this transcriptome assembly has already had obvious contamination removed. At the time of writing, Galaxy's visualizations could not be included in @@ -142,7 +143,11 @@ Availability ============ -This workflow is available to download and/or install from the main Galaxy Tool Shed: +This workflow is available from myExperiment: + +http://www.myexperiment.org/workflows/4637 + +You can also download and/or install it from the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species @@ -158,17 +163,18 @@ Citation ======== -Please cite the following paper (currently available as a preprint): +Please cite the following paper: NCBI BLAST+ integrated into Galaxy. -P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo -bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) +P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo. +GigaScience 2015, 4:1. +https://doi.org/10.1186/s13742-015-0080-7 You should also cite Galaxy, and the NCBI BLAST+ tools: BLAST+: architecture and applications. C. Camacho et al. BMC Bioinformatics 2009, 10:421. -DOI: http://dx.doi.org/10.1186/1471-2105-10-421 +https://doi.org/10.1186/1471-2105-10-421 Automated Installation @@ -188,7 +194,8 @@ ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.1.0 - Initial Tool Shed release, targetting NCBI BLAST+ 2.2.29 +v0.1.0 - Initial MyExperiment and Tool Shed release. + - Targetting NCBI BLAST+ 2.2.29 ======= ======================================================================
--- a/repository_dependencies.xml Wed Apr 08 06:06:30 2015 -0400 +++ b/repository_dependencies.xml Wed Sep 09 15:13:58 2020 +0000 @@ -1,9 +1,9 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories description="This workflow requires the NCBI BLAST+ tools etc"> - <repository changeset_revision="6119ddccd8a3" name="ncbi_blast_plus" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - <repository changeset_revision="ae709fd50581" name="fasta_to_tabular" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - <repository changeset_revision="4231c585b6dd" name="sample_seqs" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - <repository changeset_revision="2064ae2602b1" name="unique" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository owner="devteam" name="ncbi_blast_plus" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="1ebae91eb6e9"/> + <repository owner="devteam" name="fasta_to_tabular" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="5b998d13de71"/> + <repository owner="peterjc" name="sample_seqs" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="8cc7672b0fd1"/> + <repository owner="bgruening" name="unique" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="d4fb020c19ca"/> <!-- Also uses tool_id join1, Count1, and sort1 which are currently still shipped with Galaxy itself rather than via the Tool Shed --> -</repositories> +</repositories> \ No newline at end of file