Loading debian/control +1 −1 Original line number Diff line number Diff line Loading @@ -13,7 +13,7 @@ Package: kmerresistance Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: correlates mapped genes with the predicted species of WGS samples, Description: correlates mapped genes with the predicted species of WGS samples KmerResistance correlates mapped genes with the predicted species of WGS samples, where this this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for Loading debian/createmanpages 0 → 100755 +32 −0 Original line number Diff line number Diff line #!/bin/sh MANDIR=debian mkdir -p $MANDIR VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'` PROGNAME=`grep "^Package:" debian/control | head -n1 | sed 's/^Package: *//'` AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and can be used for any other usage of the program. " # If program name is different from package name or title should be # different from package short description change this here progname=${PROGNAME} echo "#!/bin/sh" > /tmp/${progname} echo "cat <<EOT" >> /tmp/${progname} /usr/bin/${progname} -h | sed 's/^#//' >> /tmp/${progname} echo "EOT" >> /tmp/${progname} chmod +x /tmp/${progname} help2man --no-info --no-discard-stderr --help-option=" " \ --name="$NAME" \ --version-string="$VERSION" /tmp/${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 cat <<EOT Please enhance the help2man output. The following web page might be helpful in doing so: http://liw.fi/manpages/ EOT debian/docs 0 → 100644 +1 −0 Original line number Diff line number Diff line README* debian/kmerresistance.1 0 → 100644 +127 −0 Original line number Diff line number Diff line .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6. .TH KMERRESISTANCE "1" "June 2018" "kmerresistance 2.0+git20180205.26467e9" "User Commands" .SH NAME kmerresistance \- correlates mapped genes with the predicted species of WGS samples .SH SYNOPSIS .SH DESCRIPTION KmerResistance correlates mapped genes with the predicted species of WGS samples, where this this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available. .SH OPTIONS .TP \fB\-i\fR Input/query file name REQUIRED .TP \fB\-o\fR Output file REQUIRED .TP \fB\-t_db\fR Template DB REQUIRED .TP \fB\-s_db\fR Species DB REQUIRED .TP \fB\-id\fR ID threshhold 70.0 .TP \fB\-dct\fR Depth correction threshhold 0.1 .TP \fB\-kma\fR alternative KMA kma .SS KMA options: .TP \fB\-i\fR Input/query file name None REQUIRED .TP \fB\-o\fR Output file None REQUIRED .TP \fB\-t_db\fR Template DB None REQUIRED .TP \fB\-k\fR Kmersize 16 .TP \fB\-e\fR evalue 0.05 .TP \fB\-delta\fR Align in pieces of delta 511 .TP \fB\-mem_mode\fR Use kmers to choose best template, and save memory False .TP \fB\-ex_mode\fR Searh kmers exhaustively False .TP \fB\-deCon\fR Remove contamination False .TP \fB\-dense\fR Do not allow insertions in assembly False .TP \fB\-ref_fsa\fR Consensus sequnce will have "n" instead of gaps False .TP \fB\-matrix\fR Print assembly matrix False .TP \fB\-mp\fR Minimum phred score 30 .TP \fB\-5p\fR Cut a constant number of nucleotides from the 5 prime. 0 .TP \fB\-Sparse\fR Run KmerFinder False .TP \fB\-ID\fR Minimum ID 1.0% .TP \fB\-ss\fR Sparse sorting (q,c,d) q .TP \fB\-shm\fR Use shared DB made by kma_shm 0 (lvl) .TP \fB\-swap\fR Swap DB to disk 0 (lvl) .TP \fB\-1t1\fR Skip HMM False .TP \fB\-boot\fR Bootstrap sequence False .TP \fB\-mrs\fR Minimum alignment score, normalized to alignment length 0.5 .TP \fB\-reward\fR Score for match 1 .TP \fB\-penalty\fR Penalty for mismatch \fB\-2\fR .TP \fB\-gapopen\fR Penalty for gap opening \fB\-3\fR .TP \fB\-gapextend\fR Penalty for gap extension \fB\-1\fR .TP \fB\-h\fR Shows this help message .SH EXAMPLES Mapping reads against resistance genes: .IP kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria .SH AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. debian/manpages 0 → 100644 +1 −0 Original line number Diff line number Diff line debian/*.1 Loading
debian/control +1 −1 Original line number Diff line number Diff line Loading @@ -13,7 +13,7 @@ Package: kmerresistance Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: correlates mapped genes with the predicted species of WGS samples, Description: correlates mapped genes with the predicted species of WGS samples KmerResistance correlates mapped genes with the predicted species of WGS samples, where this this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for Loading
debian/createmanpages 0 → 100755 +32 −0 Original line number Diff line number Diff line #!/bin/sh MANDIR=debian mkdir -p $MANDIR VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'` PROGNAME=`grep "^Package:" debian/control | head -n1 | sed 's/^Package: *//'` AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and can be used for any other usage of the program. " # If program name is different from package name or title should be # different from package short description change this here progname=${PROGNAME} echo "#!/bin/sh" > /tmp/${progname} echo "cat <<EOT" >> /tmp/${progname} /usr/bin/${progname} -h | sed 's/^#//' >> /tmp/${progname} echo "EOT" >> /tmp/${progname} chmod +x /tmp/${progname} help2man --no-info --no-discard-stderr --help-option=" " \ --name="$NAME" \ --version-string="$VERSION" /tmp/${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 cat <<EOT Please enhance the help2man output. The following web page might be helpful in doing so: http://liw.fi/manpages/ EOT
debian/kmerresistance.1 0 → 100644 +127 −0 Original line number Diff line number Diff line .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6. .TH KMERRESISTANCE "1" "June 2018" "kmerresistance 2.0+git20180205.26467e9" "User Commands" .SH NAME kmerresistance \- correlates mapped genes with the predicted species of WGS samples .SH SYNOPSIS .SH DESCRIPTION KmerResistance correlates mapped genes with the predicted species of WGS samples, where this this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available. .SH OPTIONS .TP \fB\-i\fR Input/query file name REQUIRED .TP \fB\-o\fR Output file REQUIRED .TP \fB\-t_db\fR Template DB REQUIRED .TP \fB\-s_db\fR Species DB REQUIRED .TP \fB\-id\fR ID threshhold 70.0 .TP \fB\-dct\fR Depth correction threshhold 0.1 .TP \fB\-kma\fR alternative KMA kma .SS KMA options: .TP \fB\-i\fR Input/query file name None REQUIRED .TP \fB\-o\fR Output file None REQUIRED .TP \fB\-t_db\fR Template DB None REQUIRED .TP \fB\-k\fR Kmersize 16 .TP \fB\-e\fR evalue 0.05 .TP \fB\-delta\fR Align in pieces of delta 511 .TP \fB\-mem_mode\fR Use kmers to choose best template, and save memory False .TP \fB\-ex_mode\fR Searh kmers exhaustively False .TP \fB\-deCon\fR Remove contamination False .TP \fB\-dense\fR Do not allow insertions in assembly False .TP \fB\-ref_fsa\fR Consensus sequnce will have "n" instead of gaps False .TP \fB\-matrix\fR Print assembly matrix False .TP \fB\-mp\fR Minimum phred score 30 .TP \fB\-5p\fR Cut a constant number of nucleotides from the 5 prime. 0 .TP \fB\-Sparse\fR Run KmerFinder False .TP \fB\-ID\fR Minimum ID 1.0% .TP \fB\-ss\fR Sparse sorting (q,c,d) q .TP \fB\-shm\fR Use shared DB made by kma_shm 0 (lvl) .TP \fB\-swap\fR Swap DB to disk 0 (lvl) .TP \fB\-1t1\fR Skip HMM False .TP \fB\-boot\fR Bootstrap sequence False .TP \fB\-mrs\fR Minimum alignment score, normalized to alignment length 0.5 .TP \fB\-reward\fR Score for match 1 .TP \fB\-penalty\fR Penalty for mismatch \fB\-2\fR .TP \fB\-gapopen\fR Penalty for gap opening \fB\-3\fR .TP \fB\-gapextend\fR Penalty for gap extension \fB\-1\fR .TP \fB\-h\fR Shows this help message .SH EXAMPLES Mapping reads against resistance genes: .IP kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria .SH AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
