# HG changeset patch
# User nml
# Date 1543005796 18000
# Node ID dcd43b402eb3396254c1f7109f2fdd88d1fd94ed
# Parent 9fb9fed714864f6a4dff35025bbc0536e1602124
planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
diff -r 9fb9fed71486 -r dcd43b402eb3 aacoverage.xml
--- a/aacoverage.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/aacoverage.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
Builds an aa census and returns its coverage
- quasitools
+ quasitools
+
+ @misc{GitHubquasitoolsaacoverage,
+ title = {quasitools aacoverage},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 callaavar.xml
--- a/callaavar.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/callaavar.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,15 +1,27 @@
-
+
Identifies amino acid mutations
- quasitools
+ quasitools
-
+
+
@@ -51,9 +64,19 @@
Amino Acid Variants
===================
-Identifies amino acid mutations.
+Identifies amino acid mutations for a BAM file.
+
+
]]>
+
+ @misc{GitHubquasitoolscallaavar,
+ title = {quasitools callaavar},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 callcodonvar.xml
--- a/callcodonvar.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/callcodonvar.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Identifies codon variants and non-synonymous/synonymous mutations
- quasitools
+ quasitools
-
+
+
@@ -52,5 +57,13 @@
]]>
+
+ @misc{GitHubquasitoolscallcodonvar,
+ title = {quasitools callcodonvar},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 callntvar.xml
--- a/callntvar.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/callntvar.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Identifies nucleotide variants
- quasitools
+ quasitools
-
+
@@ -30,7 +30,9 @@
@@ -44,5 +46,13 @@
]]>
+
+ @misc{GitHubquasitoolscallntvar,
+ title = {quasitools callntvar},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 complexity.xml
--- a/complexity.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/complexity.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
measures the complexity of the quasispecies reads
- quasitools
+ quasitools
-
+
+ @misc{GitHubquasitoolscomplexity,
+ title = {quasitools complexity},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
+
diff -r 9fb9fed71486 -r dcd43b402eb3 consensus.xml
--- a/consensus.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/consensus.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Generate a consensus sequence from a BAM file
- quasitools
+ quasitools
+
+ @misc{GitHubquasitoolsconsensus,
+ title = {quasitools consensus},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 distance.xml
--- a/distance.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/distance.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Calculate the evolutionary distance between viral quasispecies.
- quasitools
+ quasitools
+
Calculate the dN/dS value for each region in a bed file
- quasitools
+ quasitools
+
+ @misc{GitHubquasitoolsdnds,
+ title = {quasitools dnds},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 drmutations.xml
--- a/drmutations.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/drmutations.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
- quasitools
+ quasitools
-
-
+
+
+ @misc{GitHubquasitoolsdrmutations,
+ title = {quasitools drmutations},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
+
diff -r 9fb9fed71486 -r dcd43b402eb3 hydra.xml
--- a/hydra.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/hydra.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Identifies drug resistance within an NGS dataset
- quasitools
+ quasitools
+
+ @misc{GitHubquasitoolshydra,
+ title = {quasitools hydra},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+
diff -r 9fb9fed71486 -r dcd43b402eb3 quality.xml
--- a/quality.xml Fri Oct 12 09:16:03 2018 -0400
+++ b/quality.xml Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-
+
Performs quality control on FASTQ reads.
- quasitools
+ quasitools
+
+ @misc{GitHubquasitoolsquality,
+ title = {quasitools quality},
+ publisher = {phac-nml},
+ journal = {GitHub repository},
+ url = {https://github.com/phac-nml/quasitools},
+ }
+