# HG changeset patch
# User peterjc
# Date 1599664438 0
# Node ID 7d768ff419c085c740445e36065d10a62981033f
# Parent  a66c358bfbcf8e39001315943c2bbef266958b03
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species commit 3f9f39ad808325a11d9967980d2cb82c96d69324"

diff -r a66c358bfbcf -r 7d768ff419c0 README.rst
--- 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
 ======= ======================================================================
 
 
diff -r a66c358bfbcf -r 7d768ff419c0 repository_dependencies.xml
--- 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