# HG changeset patch
# User bebatut
# Date 1488193955 18000
# Node ID 4d1bf99ad5ef21ddfa1048ecd5ad9abaee6bd0cf
# Parent e7ed163633e1e5e7dddad6c8a647871ce0d366a4
Uploaded
diff -r e7ed163633e1 -r 4d1bf99ad5ef merge_metaphlan_tables.xml
--- a/merge_metaphlan_tables.xml Thu Feb 23 08:13:41 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
-
- MetaPhlAn2 files
-
-
- metaphlan2_macros.xml
-
-
-
-
-
- merge_metaphlan_tables.py -v
-
-
- '$output'
-]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `_.
-
-This tool performs a table join on one or more metaphlan output files
-
- ]]>
-
-
-
diff -r e7ed163633e1 -r 4d1bf99ad5ef metaphlan2.xml
--- a/metaphlan2.xml Thu Feb 23 08:13:41 2017 -0500
+++ b/metaphlan2.xml Mon Feb 27 06:12:35 2017 -0500
@@ -42,7 +42,7 @@
--bowtie2_exe `which bowtie2`
#if $db.db_selector == "cached"
- #set $path = ${db.cached_db.fields.path}
+ #set $path = $db.cached_db.fields.path
--bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
--mpa_pkl `ls $path/*.pkl`
#else
diff -r e7ed163633e1 -r 4d1bf99ad5ef metaphlan2krona.xml
--- a/metaphlan2krona.xml Thu Feb 23 08:13:41 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-
-
- output for Krona
-
-
- metaphlan2_macros.xml
-
-
-
-
-
- metaphlan2krona.py -v
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `_.
-
-This tool formats MetaPhlAn2 output to be ready for Krona.
-
- ]]>
-
-
-
diff -r e7ed163633e1 -r 4d1bf99ad5ef metaphlan_hclust_heatmap.xml
--- a/metaphlan_hclust_heatmap.xml Thu Feb 23 08:13:41 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,276 +0,0 @@
-
-
- with hierarchical clustering of both samples
-and microbial clades for MetaPhlAn2
-
-
- metaphlan2_macros.xml
-
-
-
-
-
- metaphlan_hclust_heatmap.py -v
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- output_format == "pdf"
-
-
- output_format == "png"
-
-
- output_format == "svg"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `_.
-
-This tool generates heatmaps with hierarchical clustering of both samples
-and microbial clades. The script can also subsample the number of clades to
-display based on the their nth percentile abundance value in each sample
-
- ]]>
-
-
-