# HG changeset patch
# User jjjjia
# Date 1534888388 14400
# Node ID 698579246d0df3b9d4009182c4ee5fc20d8a3906
# Parent bd6f5844d60ebb14a464b1ee60465b3a7d140592
planemo upload
diff -r bd6f5844d60e -r 698579246d0d cpo_clustalw.xml
--- a/cpo_clustalw.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_clustalw.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
- makes tree from alignment
+ Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment
clustalw
@@ -15,21 +15,6 @@
-
-
-
-
-
-
-
**Syntax**
@@ -64,4 +49,4 @@
url = {https://github.com/phac-nml/mob-suite}
}
-
\ No newline at end of file
+
diff -r bd6f5844d60e -r 698579246d0d cpo_galaxy_prediction.py
--- a/cpo_galaxy_prediction.py Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_prediction.py Tue Aug 21 17:53:08 2018 -0400
@@ -26,7 +26,7 @@
import numpy
-debug = False #True #debug skips the shell scripts and also dump out a ton of debugging messages
+debug = True #debug skips the shell scripts and also dump out a ton of debugging messages
if not debug:
#parses some parameters
@@ -645,4 +645,4 @@
Main()
end = time.time()
-print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
+print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
\ No newline at end of file
diff -r bd6f5844d60e -r 698579246d0d cpo_galaxy_predictions.xml
--- a/cpo_galaxy_predictions.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_predictions.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,6 +1,6 @@
-
- this tool parses stuff
-
+
+ This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow
+
pandas
python
@@ -19,18 +19,18 @@
]]>
-
+
-
+
-
+
diff -r bd6f5844d60e -r 698579246d0d cpo_galaxy_tree.xml
--- a/cpo_galaxy_tree.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_tree.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,9 +1,10 @@
-
- this tool makes tree
+
+ This tool makes a phylogenetic tree using data from snippy alignments, clustalw NJ tree and metadat from cpo_prediction workflow using ETE3
pandas
python
-
+ ete3
+
-
+
+ Modified MLST v2.11 to support for the cpo_prediction workflow
+
mlst
diff -r bd6f5844d60e -r 698579246d0d cpo_mobsuite.xml
--- a/cpo_mobsuite.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_mobsuite.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
-
- Type contigs and extract plasmid sequences
+
+ Modified Mobsuite (Mob-Recon) v1.4.8 to add the mob_typer for the cpo_prediction workflow
mob_suite
diff -r bd6f5844d60e -r 698579246d0d cpo_resfinder.xml
--- a/cpo_resfinder.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_resfinder.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
-
- this tool parses stuff
+
+ Modified version of Resfinder 0.8 to use custom carbapenamase database
abricate
diff -r bd6f5844d60e -r 698579246d0d cpo_rgi.xml
--- a/cpo_rgi.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_rgi.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,6 @@
-
-
+
+ Modified version of RGI to make it support galaxy without using a datatable by using the --local flag
+
rgi
python
diff -r bd6f5844d60e -r 698579246d0d cpo_snippy.xml
--- a/cpo_snippy.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_snippy.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,4 +1,5 @@
-
+
+ Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow
snippy
@@ -32,7 +33,11 @@
&&
- tar -czf out.tgz out
+ #import re
+ #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
+ mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+
+ tar -czf out.tgz ${dir_name}
]]>
diff -r bd6f5844d60e -r 698579246d0d cpo_snpdist.xml
--- a/cpo_snpdist.xml Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_snpdist.xml Tue Aug 21 17:53:08 2018 -0400
@@ -1,6 +1,7 @@
-
-
- snippy
+
+ modified snippy-dist v0.6 to the tree drawer of the cpo_predictions workflow
+
+ snp-dists