[med-svn] [Git][med-team/pplacer][master] 2 commits: DEP3
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 22 08:16:46 BST 2020
Andreas Tille pushed to branch master at Debian Med / pplacer
Commits:
4283efac by Andreas Tille at 2020-06-22T09:05:07+02:00
DEP3
- - - - -
0e64ac71 by Andreas Tille at 2020-06-22T09:16:32+02:00
Add manpage
- - - - -
7 changed files:
- + debian/createmanpages
- + debian/guppy.1
- + debian/manpages
- debian/patches/fix_makefile.patch
- debian/patches/ocamlbuild
- + debian/pplacer.1
- + debian/rppr.1
Changes:
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,40 @@
+#!/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: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="place reads on a phylogenetic tree" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=guppy
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=rppr
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="tool for working with reference packages" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/guppy.1
=====================================
@@ -0,0 +1,153 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH GUPPY "1" "June 2020" "guppy 1.1~alpha19" "User Commands"
+.SH NAME
+guppy \- Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output
+.SH SYNOPSIS
+.B guppy
+<command> [options]
+.SH OPTIONS
+.SS visualization
+.TP
+fat
+makes trees with edges fattened in proportion to the number of reads
+.TP
+heat
+maps an an arbitrary vector of the correct length to the tree
+.TP
+sing
+makes one tree for each query sequence, showing uncertainty
+.TP
+tog
+makes a tree with each of the reads represented as a pendant edge
+.SS statistical comparison
+.TP
+bary
+draws the barycenter of a placement collection on the reference tree
+.TP
+edpl
+calculates the EDPL uncertainty values for a collection of pqueries
+.TP
+epca
+performs edge principal components
+.TP
+error
+finds the error between two placefiles
+.TP
+fpd
+calculates various alpha diversity metrics of placefiles
+.TP
+indep_c
+calculates the independent contrasts of pqueries
+.TP
+kr
+calculates the Kantorovich\-Rubinstein distance and corresponding p\-values
+.TP
+kr_heat
+makes a heat tree
+.TP
+lpca
+performs length principal components
+.TP
+mcl
+cluster pqueries using Markov clustering via MCL
+.TP
+pmlpca
+performs poor\-man's length principal components
+.TP
+rarefact
+calculates phylogenetic rarefaction curves
+.TP
+splitify
+writes out differences of masses for the splits of the tree
+.TP
+squash
+performs squash clustering
+.TP
+unifrac
+calculates unifrac on two or more placefiles
+.SH classification
+.TP
+classify
+outputs classification information in SQLite format
+.TP
+to_rdp
+convert a reference package to a format RDP wants
+.SS utilities
+.TP
+adcl
+calculates ADCL for each pquery in a placefile
+.TP
+check
+checks placefiles for common problems
+.TP
+compress
+compresses a placefile's pqueries
+.TP
+demulti
+splits apart placements with multiplicity, undoing a round procedure
+.TP
+distmat
+prints out a pairwise distance matrix between the edges
+.TP
+filter
+filters one or more placefiles by placement name
+.TP
+info
+writes the number of leaves of the reference tree and the number of pqueries
+.TP
+islands
+finds the mass islands of one or more pqueries
+.TP
+merge
+merges placefiles together
+.TP
+mft
+Multi\-Filter and Transform placefiles
+.TP
+ograph
+finds the overlap graph of one or more pqueries
+.TP
+placemat
+prints out a pairwise distance matrix between placements
+.TP
+rarefy
+performs rarefaction on collections of placements
+.TP
+redup
+restores duplicates to deduped placefiles
+.TP
+round
+clusters the placements by rounding branch lengths
+.TP
+to_csv
+turns a placefile into a csv file
+.TP
+to_json
+converts old\-style .place files to .jplace placement files
+.TP
+trim
+trims placefiles down to only containing an informative subset of the mass
+.PP
+To get more help about a given command, type guppy COMMAND \fB\-\-help\fR
+.SS "Additional options"
+.TP
+\fB\-\-version\fR
+Print version and exit
+.TP
+\fB\-\-cmds\fR
+Print a list of the available commands.
+.TP
+\fB\-\-batch\fR
+Run the provided batch file of guppy commands
+.TP
+\fB\-\-quiet\fR
+Don't write messages to stdout (unless explicitly requested).
+.TP
+\fB\-\-help\fR
+Display this list of options and subcommands
+.TP
+\fB\-help\fR
+Display this list of options and subcommands
+.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
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/fix_makefile.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 22 May 2020 07:19:29 +0200
+Description: Avoid calling git to obtain version
+
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
=====================================
debian/patches/ocamlbuild
=====================================
@@ -1,3 +1,8 @@
+Author: Ralf Treinen
+ Shayan Doust
+Last-Update: 2020-06-21 22:04:51 +0100
+Description: Build with recent ocaml
+
--- pplacer.orig/myocamlbuild.ml
+++ pplacer/myocamlbuild.ml
@@ -19,10 +19,7 @@
=====================================
debian/pplacer.1
=====================================
@@ -0,0 +1,158 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH PPLACER "1" "June 2020" "pplacer 1.1~alpha19" "User Commands"
+.SH NAME
+pplacer \- place reads on a phylogenetic tree
+.SH SYNOPSIS
+.B pplacer
+[options] [alignment]
+.SH OPTIONS
+.TP
+\fB\-c\fR
+Specify the path to the reference package.
+.TP
+\fB\-t\fR
+Specify the reference tree filename.
+.TP
+\fB\-r\fR
+Specify the reference alignment filename.
+.TP
+\fB\-s\fR
+Supply a phyml stats.txt or a RAxML info file giving the model parameters.
+.TP
+\fB\-d\fR
+Specify the directory containing the reference information.
+.TP
+\fB\-p\fR
+Calculate posterior probabilities.
+.TP
+\fB\-m\fR
+Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.
+.TP
+\fB\-\-model\-freqs\fR
+Use model frequencies instead of reference alignment frequencies.
+.TP
+\fB\-\-gamma\-cats\fR
+Number of categories for discrete gamma model.
+.TP
+\fB\-\-gamma\-alpha\fR
+Specify the shape parameter for a discrete gamma model.
+.TP
+\fB\-\-ml\-tolerance\fR
+1st stage branch len optimization tolerance (2nd stage to 1e\-5). Default: 0.01.
+.TP
+\fB\-\-pp\-rel\-err\fR
+Relative error for the posterior probability calculation. Default is 0.01.
+.TP
+\fB\-\-unif\-prior\fR
+Use a uniform prior rather than exponential.
+.TP
+\fB\-\-inform\-prior\fR
+Use an informative exponential prior based on rooted distance to leaves.
+.TP
+\fB\-\-prior\-lower\fR
+Lower bound for the informative prior mean. Default is 0.
+.TP
+\fB\-\-start\-pend\fR
+Starting pendant branch length. Default is 0.1.
+.TP
+\fB\-\-max\-pend\fR
+Set the maximum ML pendant branch length. Default is 2.
+.TP
+\fB\-\-fig\-cutoff\fR
+The cutoff for determining figs. Default is 0; specify 0 to disable.
+.TP
+\fB\-\-fig\-eval\-all\fR
+Evaluate all likelihoods to ensure that the best location was selected.
+.TP
+\fB\-\-fig\-eval\-discrepancy\-tree\fR
+Write out a tree showing the discrepancies between the best complete and observed locations.
+.TP
+\fB\-\-fig\-tree\fR
+Write out a tree showing the figs on the tree.
+.TP
+\fB\-\-max\-strikes\fR
+Maximum number of strikes for baseball. 0 \-> no ball playing. Default is 6.
+.TP
+\fB\-\-strike\-box\fR
+Set the size of the strike box in log likelihood units. Default is 3.
+.TP
+\fB\-\-max\-pitches\fR
+Set the maximum number of pitches for baseball. Default is 40.
+.TP
+\fB\-\-fantasy\fR
+Desired likelihood cutoff for fantasy baseball mode. 0 \-> no fantasy.
+.TP
+\fB\-\-fantasy\-frac\fR
+Fraction of fragments to use when running fantasy baseball. Default is 0.1.
+.TP
+\fB\-\-write\-masked\fR
+Write alignment masked to the region without gaps in the query.
+.TP
+\fB\-\-verbosity\fR
+Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.
+.TP
+\fB\-\-out\-dir\fR
+Specify the directory to write place files to.
+.TP
+\fB\-o\fR
+Specify the output file name
+.TP
+\fB\-\-pretend\fR
+Only check out the files then report. Do not run the analysis.
+.TP
+\fB\-\-check\-like\fR
+Write out the likelihood of the reference tree, calculated two ways.
+.TP
+\fB\-j\fR
+The number of child processes to spawn when doing placements. Default is 2.
+.TP
+\fB\-\-timing\fR
+Display timing information after the pplacer run finishes.
+.TP
+\fB\-\-no\-pre\-mask\fR
+Don't pre\-mask sequences before placement.
+.TP
+\fB\-\-write\-pre\-masked\fR
+Write out the pre\-masked sequences to the specified fasta file before placement.
+.TP
+\fB\-\-map\-mrca\fR
+Specify a file to write out MAP sequences for MRCAs and corresponding placements.
+.TP
+\fB\-\-map\-mrca\-min\fR
+Specify cutoff for inclusion in MAP sequence file. Default is 0.8.
+.TP
+\fB\-\-map\-identity\fR
+Add the percent identity of the query sequence to the nearest MAP sequence to each placement.
+.TP
+\fB\-\-keep\-at\-most\fR
+The maximum number of placements we keep. Default is 7.
+.TP
+\fB\-\-keep\-factor\fR
+Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01.
+.TP
+\fB\-\-mrca\-class\fR
+Classify with MRCAs instead of a painted tree.
+.TP
+\fB\-\-groups\fR
+Split query alignment into the specified number of groups.
+.TP
+\fB\-\-always\-refine\fR
+Always refine the model before placing.
+.TP
+\fB\-\-mmap\-file\fR
+Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.
+.TP
+\fB\-\-discard\-nonoverlapped\fR
+When pre\-masking, silently discard sequences which don't overlap the mask.
+.TP
+\fB\-\-version\fR
+Write out the version number and exit.
+.TP
+\fB\-help\fR
+Display this list of options
+.TP
+\fB\-\-help\fR
+Display this list of options
+.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/rppr.1
=====================================
@@ -0,0 +1,72 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH RPPR "1" "June 2020" "rppr 1.1~alpha19" "User Commands"
+.SH NAME
+rppr \- tool for working with reference packages
+.SH SYNOPSIS
+.B rppr
+<command> [options]
+.SH OPTIONS
+.SS "available commands"
+.TP
+check
+checks a reference package
+.TP
+convex_taxids
+determines convex tax_ids per\-rank in a refpkg
+.TP
+convexify
+identifies minimal leaf set to cut for taxonomic concordance
+.TP
+infer
+infers classifications of unclassified sequences in a reference package
+.TP
+info
+gives information about a reference package
+.TP
+min_adcl
+finds a good collection of sequences to cut from a placefile's ref tree
+.TP
+min_adcl_tree
+finds a good collection of sequences to cut from a tree
+.TP
+pdprune
+prunes the tree to maximize PD
+.TP
+prep_db
+makes SQL enabling taxonomic querying of placement results
+.TP
+prepsim
+makes a simulation by taking out taxids and turning them into fake placements
+.TP
+reclass
+reclassifies nonconvex sequences in a reference package
+.TP
+ref_tree
+writes a taxonomically annotated reference tree and an induced taxonomic tree
+.TP
+reroot
+reroots a given reference package in place
+.PP
+To get more help about a given command, type rppr COMMAND \fB\-\-help\fR
+.SS "Additional options"
+.TP
+\fB\-\-version\fR
+Print version and exit
+.TP
+\fB\-\-cmds\fR
+Print a list of the available commands.
+.TP
+\fB\-\-batch\fR
+Run the provided batch file of guppy commands
+.TP
+\fB\-\-quiet\fR
+Don't write messages to stdout (unless explicitly requested).
+.TP
+\fB\-\-help\fR
+Display this list of options and subcommands
+.TP
+\fB\-help\fR
+Display this list of options and subcommands
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1
--
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/92732f227ecef23f235fce54cd28d410a9c2a634...0e64ac7167f17ccf06da66cfdbb489abc9de6dd1
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