[med-svn] [Git][med-team/radiant][master] 7 commits: d/watch: Fix watch regex
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed Jun 2 21:22:57 BST 2021
Nilesh Patra pushed to branch master at Debian Med / radiant
Commits:
756420c8 by Nilesh Patra at 2021-06-03T01:16:43+05:30
d/watch: Fix watch regex
- - - - -
a7f91b98 by Nilesh Patra at 2021-06-03T01:26:24+05:30
New upstream version 2.8+dfsg
- - - - -
09045f0f by Nilesh Patra at 2021-06-03T01:28:01+05:30
Update upstream source from tag 'upstream/2.8+dfsg'
Update to upstream version '2.8+dfsg'
with Debian dir 512a6f008f76434246a917d2cd7c5a054f4cafc0
- - - - -
1264dc39 by Nilesh Patra at 2021-06-03T01:45:29+05:30
Update Manpages
- - - - -
f9b5da90 by Nilesh Patra at 2021-06-03T01:46:27+05:30
Declare compliance with policy 4.5.1
- - - - -
c51a69df by Nilesh Patra at 2021-06-03T01:46:58+05:30
Bump watch file version to 4
- - - - -
8aa46647 by Nilesh Patra at 2021-06-03T01:49:16+05:30
Interim changelog entry
- - - - -
30 changed files:
- KronaTools/lib/KronaTools.pm
- KronaTools/scripts/ClassifyBLAST.pl
- KronaTools/scripts/GetTaxIDFromAcc.pl
- KronaTools/scripts/GetTaxInfo.pl
- KronaTools/scripts/ImportBLAST.pl
- KronaTools/scripts/accession2taxid.make
- KronaTools/src/krona-2.0.js
- debian/changelog
- debian/control
- debian/ktClassifyBLAST.1
- debian/ktGetContigMagnitudes.1
- debian/ktGetLCA.1
- debian/ktGetLibPath.1
- debian/ktGetTaxIDFromAcc.1
- debian/ktGetTaxInfo.1
- debian/ktImportBLAST.1
- debian/ktImportDiskUsage.1
- debian/ktImportEC.1
- debian/ktImportFCP.1
- debian/ktImportGalaxy.1
- debian/ktImportKrona.1
- debian/ktImportMETAREP-EC.1
- debian/ktImportMGRAST.1
- debian/ktImportPhymmBL.1
- debian/ktImportRDP.1
- debian/ktImportRDPComparison.1
- debian/ktImportTaxonomy.1
- debian/ktImportText.1
- debian/ktImportXML.1
- debian/watch
Changes:
=====================================
KronaTools/lib/KronaTools.pm
=====================================
@@ -114,6 +114,8 @@ my %optionFormats =
'e=i',
'factor' =>
'e=f',
+ 'includeUnk' =>
+ 'f',
'include' =>
'i',
'cellular' =>
@@ -189,6 +191,7 @@ my %optionDescriptions =
'hueGood' => 'Hue (0-360) for "good" scores.',
'percentIdentity' => 'Use percent identity for average scores instead of log[10] e-value.',
'include' => 'Include a wedge for queries with no hits.',
+ 'includeUnk' => 'If any best hits have unknown accessions, force classification to root instead of ignoring them.',
'local' => 'Use resources from the local KronaTools installation instead of bundling them with charts (charts will be smaller but will only work on this computer).',
'magCol' => 'Column of input files to use as magnitude. If magnitude files are specified, their magnitudes will override those in this column.',
'minConfidence' => 'Minimum confidence. Each query sequence will only be added to taxa that were predicted with a confidence score of at least this value.',
@@ -915,7 +918,7 @@ sub classifyBlast
# taxonomically classifies BLAST results based on LCA (or random selection)
# of 'best' hits.
#
- # Options used: bitScore, factor, include, percentIdentity, random, score
+ # Options used: bitScore, factor, include, percentIdentity, random, score, includeUnk
my # parameters
(
@@ -1008,21 +1011,32 @@ sub classifyBlast
last; # EOF
}
- my $acc = getAccFromSeqID($hitID);
-
- if ( ! defined $acc )
- {
- $lastQueryID = $queryID;
- next;
- }
-
if # this is a 'best' hit if...
(
- $queryID ne $lastQueryID || # new query ID (including null at EOF)
+ $ties == 0 || # first hit
$bitScore >= $topScore - $options{'threshold'} || # within score threshold
$options{'factor'} && $eVal <= $options{'factor'} * $topEVal # within e-val factor
)
{
+ my $acc = getAccFromSeqID($hitID);
+ my $newTaxID = getTaxIDFromAcc($acc);
+
+ if
+ (
+ ! defined $acc ||
+ ! $options{'includeUnk'} && (! $newTaxID || ! taxIDExists($newTaxID))
+ )
+ {
+ $lastQueryID = $queryID;
+ next;
+ }
+
+ if ( $ties == 0 )
+ {
+ $topScore = $bitScore;
+ $topEVal = $eVal;
+ }
+
# add score for average
#
if ( $options{'percentIdentity'} )
@@ -1055,8 +1069,6 @@ sub classifyBlast
int(rand($ties)) == 0 # randomly chosen to replace other hit
)
{
- my $newTaxID = getTaxIDFromAcc($acc);
-
if ( ! $newTaxID || ! taxIDExists($newTaxID) )
{
$newTaxID = 1;
@@ -1073,12 +1085,6 @@ sub classifyBlast
}
}
- if ( $queryID ne $lastQueryID )
- {
- $topScore = $bitScore;
- $topEVal = $eVal;
- }
-
$lastQueryID = $queryID;
}
@@ -1218,6 +1224,11 @@ sub getTaxInfo
$tax = int($tax);
+ if ( $tax == 0 )
+ {
+ return ('', '', '', '', '');
+ }
+
if ( defined $taxInfoByID{$tax} )
{
return @{$taxInfoByID{$tax}};
@@ -1822,6 +1833,11 @@ sub taxLowestCommonAncestor
#
foreach my $node ( @nodes )
{
+ if ( $node == 1)
+ {
+ return 1; # early out if any nodes are root
+ }
+
while ( getTaxDepth($node) > $minDepth )
{
$node = getTaxParent($node);
=====================================
KronaTools/scripts/ClassifyBLAST.pl
=====================================
@@ -21,6 +21,7 @@ my @options =
qw(
out
threshold
+ includeUnk
random
percentIdentity
bitScore
=====================================
KronaTools/scripts/GetTaxIDFromAcc.pl
=====================================
@@ -23,6 +23,7 @@ my $help;
my $prepend;
my $append;
my $tax;
+my $field = 1;
GetOptions
(
@@ -30,7 +31,8 @@ GetOptions
'help' => \$help,
'p' => \$prepend,
'a' => \$append,
- 'tax=s' => \$tax
+ 'tax=s' => \$tax,
+ 'f=i' => \$field
);
if ( defined $tax )
@@ -59,13 +61,17 @@ Usage:
Fasta tag example:
- grep ">" sequence
+ grep ">" sequence | ktGetTaxIDFromAcc > sequence.tax
Options:
- -p Prepend tax IDs to the original lines (separated by tabs).
+ [-p] Prepend tax IDs to the original lines (separated by tabs).
- -a Append tax IDs to the original lines (separated by tabs).
+ [-a] Append tax IDs to the original lines (separated by tabs).
+
+ [-f] <integer> Field of accessions. [Default: \'1\']
+
+ [-tax <string> Path to directory containing a taxonomy database to use.
';
exit;
@@ -83,6 +89,11 @@ if ( @ARGV == 0 )
{
$stdin = 1;
}
+elsif ( $field != 1 )
+{
+ print STDERR "ERROR: -f requires stdin, not command line input.\n";
+ exit 1;
+}
while ( my $in = $stdin ? <STDIN> : shift @ARGV )
{
@@ -99,7 +110,8 @@ while ( my $in = $stdin ? <STDIN> : shift @ARGV )
print "$in\t";
}
- print getTaxIDFromAcc(getAccFromSeqID($in));
+ my $acc = (split /\t/, $in)[$field - 1];
+ print getTaxIDFromAcc(getAccFromSeqID($acc));
if ( $prepend )
{
=====================================
KronaTools/scripts/GetTaxInfo.pl
=====================================
@@ -17,12 +17,16 @@ my $totalMag;
my $prepend;
my $append;
my $tax;
+my $field = 1;
GetOptions
(
'h' => \$help,
'help' => \$help,
- 'tax=s' => \$tax
+ 'p' => \$prepend,
+ 'a' => \$append,
+ 'tax=s' => \$tax,
+ 'f=i' => \$field
);
if ( defined $tax )
@@ -43,6 +47,9 @@ Description:
[>,@]). If taxonomy information was not found for a given input line, the
output line will be only the taxonomy ID, which will be 0 if it was
looked up from an accession but not found.
+
+ Output fields are:
+ taxID depth parent rank name
Usage:
@@ -56,11 +63,24 @@ Usage:
grep ">" sequence.fasta | ktGetTaxInfo
+Options:
+
+ [-p] Prepend tax info to the original lines (separated by tabs).
+
+ [-a] Append tax info to the original lines (separated by tabs).
+
+ [-f] <integer> Field of accessions. [Default: \'1\']
+
+ [-tax <string> Path to directory containing a taxonomy database to use.
+
';
exit;
}
-print "#taxID\tdepth\tparent\trank\tname\n";
+if ( ! $prepend && ! $append )
+{
+ print "#taxID\tdepth\tparent\trank\tname\n";
+}
my $stdin;
@@ -79,7 +99,19 @@ while ( my $in = $stdin ? <STDIN> : shift @ARGV )
next;
}
- print join "\t", getTaxInfo(getTaxIDFromAcc(getAccFromSeqID($in)));
+ if ( $append )
+ {
+ print "$in\t";
+ }
+
+ my $acc = (split /\t/, $in)[$field - 1];
+ print join "\t", getTaxInfo(getTaxIDFromAcc(getAccFromSeqID($acc)));
+
+ if ( $prepend )
+ {
+ print "\t$in";
+ }
+
print "\n";
}
=====================================
KronaTools/scripts/ImportBLAST.pl
=====================================
@@ -28,6 +28,7 @@ qw(
name
threshold
include
+ includeUnk
random
percentIdentity
bitScore
=====================================
KronaTools/scripts/accession2taxid.make
=====================================
@@ -6,25 +6,34 @@ ACC2TAXID=\
nucl_wgs.accession2taxid \
prot.accession2taxid
-ACC2TAXID_SORTED=$(ACC2TAXID:.accession2taxid=.accession2taxid.sorted)
+ACC2TAXID_FMT=$(ACC2TAXID:.accession2taxid=.accession2taxid.fmt)
-../all.accession2taxid.sorted : $(ACC2TAXID_SORTED)
- @echo "Merging sorted..."
- @LC_ALL=C sort -m $(ACC2TAXID_SORTED) > $@
- @rm $(ACC2TAXID_SORTED)
+../all.accession2taxid.sorted : $(ACC2TAXID_FMT)
+ @echo "Merging..."
+ @LC_ALL=C TMPDIR=. sort -m $(ACC2TAXID_FMT) > $@
+ @rm $(ACC2TAXID_FMT)
-SORT := grep -v accession | sed 's/\.[[:digit:]]*//' | LC_ALL=C sort
+FORMAT4 := grep -v accession | cut -f 1,3
+FORMAT2 := grep -v accession | sed 's/\.[[:digit:]]*//;s/ / /'
-%.accession2taxid.sorted : %.accession2taxid
- @echo "Sorting $<..."
- @cut -f 2,3 $< | ${SORT} > $@
+%.accession2taxid.fmt : %.accession2taxid
+ @echo "Formatting $<..."
+ @if [ `awk '{print NF; exit}' $<` = "2" ]; then \
+ cat $< | ${FORMAT2} > $@; \
+ else \
+ cat $< | ${FORMAT4} > $@; \
+ fi
ifneq ("${PRESERVE}", "1")
@rm $<
endif
-%.accession2taxid.sorted : %.accession2taxid.gz
- @echo "Sorting $<..."
- @gunzip -c $< | cut -f 2,3 | ${SORT} > $@
+%.accession2taxid.fmt : %.accession2taxid.gz
+ @echo "Formatting $<..."
+ @if [ `gunzip -c $< | awk '{print NF; exit}'` = "2" ]; then \
+ gunzip -c $< | ${FORMAT2} > $@; \
+ else \
+ gunzip -c $< | ${FORMAT4} > $@; \
+ fi
ifneq ("${PRESERVE}", "1")
@rm $<
endif
=====================================
KronaTools/src/krona-2.0.js
=====================================
@@ -5760,10 +5760,18 @@ function setCallBacks()
}
image = document.getElementById('hiddenImage');
- image.onload = function()
+
+ if ( image.complete )
{
hiddenPattern = context.createPattern(image, 'repeat');
}
+ else
+ {
+ image.onload = function()
+ {
+ hiddenPattern = context.createPattern(image, 'repeat');
+ }
+ }
var loadingImageElement = document.getElementById('loadingImage');
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+radiant (2.8+dfsg-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * d/watch: Fix watch regex
+ * New upstream version 2.8+dfsg
+ * Update Manpages
+ * Declare compliance with policy 4.5.1
+ * Bump watch file version to 4
+
+ -- Nilesh Patra <nilesh at debian.org> Thu, 03 Jun 2021 01:48:58 +0530
+
radiant (2.7.1+dfsg-4) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/radiant
Vcs-Git: https://salsa.debian.org/med-team/radiant.git
Homepage: https://github.com/marbl/Krona
=====================================
debian/ktClassifyBLAST.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTCLASSIFYBLAST "1" "August 2020" "ktClassifyBLAST 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTCLASSIFYBLAST "1" "June 2021" "ktClassifyBLAST 2.8" "User Commands"
.SH NAME
ktClassifyBLAST \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
@@ -27,6 +27,9 @@ Output file name. [Default: 'blast.taxonomy.tab']
Threshold for bit score differences when determining "best" hits. Hits with scores that are within this distance of the highest score will be included when computing the lowest common ancestor (or picking randomly if
\fB\-r\fR is specified). [Default: '3']
.TP
+[\-f]
+If any best hits have unknown accessions, force classification to root instead of ignoring them.
+.TP
[\-r]
Pick from the best hits randomly instead of finding the lowest common ancestor.
.TP
=====================================
debian/ktGetContigMagnitudes.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTGETCONTIGMAGNITUDES "1" "August 2020" "ktGetContigMagnitudes 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTGETCONTIGMAGNITUDES "1" "June 2021" "ktGetContigMagnitudes 2.8" "User Commands"
.SH NAME
ktGetContigMagnitudes \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktGetLCA.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTGETLCA "1" "August 2020" "ktGetLCA 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTGETLCA "1" "June 2021" "ktGetLCA 2.8" "User Commands"
.SH NAME
ktGetLCA \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktGetLibPath.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTGETLIBPATH "1" "August 2020" "ktGetLibPath 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTGETLIBPATH "1" "June 2021" "ktGetLibPath 2.8" "User Commands"
.SH NAME
ktGetLibPath \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktGetTaxIDFromAcc.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTGETTAXIDFROMACC "1" "August 2020" "ktGetTaxIDFromAcc 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTGETTAXIDFROMACC "1" "June 2021" "ktGetTaxIDFromAcc 2.8" "User Commands"
.SH NAME
ktGetTaxIDFromAcc \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
@@ -21,11 +21,17 @@ ktGetTaxIDFromAcc A00001.1 A00002.1
.IP
Fasta tag example:
.IP
-grep ">" sequence
+grep ">" sequence | ktGetTaxIDFromAcc > sequence.tax
.SH OPTIONS
.TP
-\fB\-p\fR
+[\-p]
Prepend tax IDs to the original lines (separated by tabs).
.TP
-\fB\-a\fR
+[\-a]
Append tax IDs to the original lines (separated by tabs).
+.TP
+[\-f] <integer>
+Field of accessions. [Default: '1']
+.TP
+[\-tax <string>
+Path to directory containing a taxonomy database to use.
=====================================
debian/ktGetTaxInfo.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTGETTAXINFO "1" "August 2020" "ktGetTaxInfo 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTGETTAXINFO "1" "June 2021" "ktGetTaxInfo 2.8" "User Commands"
.SH NAME
ktGetTaxInfo \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
@@ -13,6 +13,9 @@ notation (e.g. "gi|12345|xx|ABC123.1|", ignoring fasta/fastq tag markers
[>,@]). If taxonomy information was not found for a given input line, the
output line will be only the taxonomy ID, which will be 0 if it was
looked up from an accession but not found.
+.IP
+Output fields are:
+taxID depth parent rank name
.PP
Usage:
.IP
@@ -25,3 +28,16 @@ ktGetTaxInfo A00001.1 "gi|2|emb|A00002.1|" 9606
Fasta tag example:
.IP
grep ">" sequence.fasta | ktGetTaxInfo
+.SH OPTIONS
+.TP
+[\-p]
+Prepend tax info to the original lines (separated by tabs).
+.TP
+[\-a]
+Append tax info to the original lines (separated by tabs).
+.TP
+[\-f] <integer>
+Field of accessions. [Default: '1']
+.TP
+[\-tax <string>
+Path to directory containing a taxonomy database to use.
=====================================
debian/ktImportBLAST.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTBLAST "1" "August 2020" "ktImportBLAST 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTBLAST "1" "June 2021" "ktImportBLAST 2.8" "User Commands"
.SH NAME
ktImportBLAST \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
@@ -40,6 +40,9 @@ if \fB\-r\fR is specified). [Default: '3']
[\-i]
Include a wedge for queries with no hits.
.TP
+[\-f]
+If any best hits have unknown accessions, force classification to root instead of ignoring them.
+.TP
[\-r]
Pick from the best hits randomly instead of finding the lowest common ancestor.
.TP
=====================================
debian/ktImportDiskUsage.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTDISKUSAGE "1" "August 2020" "ktImportDiskUsage 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTDISKUSAGE "1" "June 2021" "ktImportDiskUsage 2.8" "User Commands"
.SH NAME
ktImportDiskUsage \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportEC.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTEC "1" "August 2020" "ktImportEC 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTEC "1" "June 2021" "ktImportEC 2.8" "User Commands"
.SH NAME
ktImportEC \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportFCP.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTFCP "1" "August 2020" "ktImportFCP 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTFCP "1" "June 2021" "ktImportFCP 2.8" "User Commands"
.SH NAME
ktImportFCP \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportGalaxy.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTGALAXY "1" "August 2020" "ktImportGalaxy 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTGALAXY "1" "June 2021" "ktImportGalaxy 2.8" "User Commands"
.SH NAME
ktImportGalaxy \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportKrona.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTKRONA "1" "August 2020" "ktImportKrona 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTKRONA "1" "June 2021" "ktImportKrona 2.8" "User Commands"
.SH NAME
ktImportKrona \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportMETAREP-EC.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTMETAREP-EC "1" "August 2020" "ktImportMETAREP-EC 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTMETAREP-EC "1" "June 2021" "ktImportMETAREP-EC 2.8" "User Commands"
.SH NAME
ktImportMETAREP-EC \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportMGRAST.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTMGRAST "1" "August 2020" "ktImportMGRAST 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTMGRAST "1" "June 2021" "ktImportMGRAST 2.8" "User Commands"
.SH NAME
ktImportMGRAST \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportPhymmBL.1
=====================================
@@ -1,9 +1,10 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTPHYMMBL "1" "August 2020" "ktImportPhymmBL 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTPHYMMBL "1" "June 2021" "ktImportPhymmBL 2.8" "User Commands"
.SH NAME
ktImportPhymmBL \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
.IP
+.PP
Creates a Krona chart of Phymm or PhymmBL results. Note: Since confidence scores are not given for species/subspecies classifications, they inheret confidence scores from genus classifications.
.IP
.PP
=====================================
debian/ktImportRDP.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTRDP "1" "August 2020" "ktImportRDP 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTRDP "1" "June 2021" "ktImportRDP 2.8" "User Commands"
.SH NAME
ktImportRDP \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportRDPComparison.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTRDPCOMPARISON "1" "August 2020" "ktImportRDPComparison 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTRDPCOMPARISON "1" "June 2021" "ktImportRDPComparison 2.8" "User Commands"
.SH NAME
ktImportRDPComparison \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportTaxonomy.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTTAXONOMY "1" "August 2020" "ktImportTaxonomy 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTTAXONOMY "1" "June 2021" "ktImportTaxonomy 2.8" "User Commands"
.SH NAME
ktImportTaxonomy \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportText.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTTEXT "1" "August 2020" "ktImportText 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTTEXT "1" "June 2021" "ktImportText 2.8" "User Commands"
.SH NAME
ktImportText \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/ktImportXML.1
=====================================
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KTIMPORTXML "1" "August 2020" "ktImportXML 2.7.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH KTIMPORTXML "1" "June 2021" "ktImportXML 2.8" "User Commands"
.SH NAME
ktImportXML \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://github.com/marbl/Krona/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+ https://github.com/marbl/Krona/releases .*/archive/.*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
View it on GitLab: https://salsa.debian.org/med-team/radiant/-/compare/6260d2ad98a4f62e36a6e910cf99256e38b746b6...8aa46647fea4e01c0f2af41d54f38e98167ccf89
--
View it on GitLab: https://salsa.debian.org/med-team/radiant/-/compare/6260d2ad98a4f62e36a6e910cf99256e38b746b6...8aa46647fea4e01c0f2af41d54f38e98167ccf89
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