From cb6136a78cb044cd9c4721430e6aa764b3951963 Mon Sep 17 00:00:00 2001
From: Shaman <shaman.narayanasamy@uni.lu>
Date: Thu, 26 Mar 2015 22:58:45 +0100
Subject: [PATCH] Some change
---
rules/Analysis/MGMT.rules | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/rules/Analysis/MGMT.rules b/rules/Analysis/MGMT.rules
index e3e7aff..1db5c0a 100644
--- a/rules/Analysis/MGMT.rules
+++ b/rules/Analysis/MGMT.rules
@@ -537,22 +537,20 @@ rule ANALYSIS_KRONA_PLOT_MG:
"%s/benchmarks/ANALYSIS_KRONA_PLOT.json" % AN_OUT
input:
"%s/MG.prokkaID2ec.txt" % AN_OUT,
-# "%s/ec2pwy.txt" % U_OUT,
-# "%s/pwy2hierarchy.txt" % U_OUT,
+ "%s/ec2pwy.txt" % U_OUT,
+ "%s/pwy2hierarchy.txt" % U_OUT,
"%s/MG.gene_depth.avg" % AN_OUT,
"%s/MG.gene.len" % AN_OUT
output:
-# "%s/results/MG.gene_kegg_krona.txt" % AN_OUT,
-# "%s/results/MG.gene_kegg_krona.html" % AN_OUT
- "%s/krona.done" % AN_OUT
+ "%s/results/MG.gene_kegg_krona.txt" % AN_OUT,
+ "%s/results/MG.gene_kegg_krona.html" % AN_OUT
shell:
"""
echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
echo {input}
echo {output[0]}
- touch {output[0]}
+ python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -H {input[1]} -m {input[2]} -c {input[3]} -L {input[4]} -o {output[0]}
+ ktImportText -o {output[1]} {output[0]}
"""
-# python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[4]} -o {output[0]}
-# ktImportText -o {output[1]} {output[0]}
#rule ANALYSIS_KRONA_PLOT_MT:
--
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