Mercurial > repos > okorol > itsx
diff ITSx.xml @ 0:f82c70f54bd7 draft
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author | okorol |
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date | Tue, 24 Mar 2015 12:02:48 -0400 |
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children | b433586432d7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx.xml Tue Mar 24 12:02:48 2015 -0400 @@ -0,0 +1,172 @@ +<tool id="ITSx" name="ITSx Extractor" version="1.0.6"> + + <description> + ITSx -- Identifies ITS sequences and extracts the ITS region + </description> + + <command interpreter="perl"> + ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset + </command> + <requirements> + <requirement type="package" version="3.1b1">hmmer</requirement> + </requirements> + <inputs> + <param name="input" type="data" format="fasta" label="Input Fasta"/> + <param name="cpu" type="integer" value="1" label="cpu"/> + <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Checks both DNA strands against the database"/> + <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/> + <param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/> + <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/> + </inputs> + + <outputs> + <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/> + <data name="ITS2" format="fasta" label="Extracted ITS2 Fasta File" from_work_dir="ITSx_out.ITS2.fasta"/> + <data name="fullfasta" format="fasta" label="Full Fasta of ITS extracted" from_work_dir="ITSx_out.full.fasta"/> + <data name="graph" format="txt" label="Graph of ITS regions" from_work_dir="ITSx_out.graph"/> + <data name="nodetect" format="fasta" label="No ITS region" from_work_dir="ITSx_out_no_detections.fasta"/> + <data name="positions" format="tabular" label="ITSx feature positions" from_work_dir="ITSx_out.positions.txt"/> + <data name="problematic" format="tabular" label="Problematic sequences" from_work_dir="ITSx_out.problematic.txt"/> + <data name="summary" format="txt" label="ITSx summary" from_work_dir="ITSx_out.summary.txt"/> + <data name="extractions" format="tabular" label="ITSx extraction results" from_work_dir="ITSx_out.extraction.results"/> + </outputs> + + <stdio> + <regex match="ITSx" source="both" level="log"/> + <regex match="analysis" source="both" level="log"/> + <regex match="ERROR" source="both" level="fatal"/> + <regex match="error" source="both" level="fatal"/> + </stdio> + + <test></test> + <help> +ITSx -- Identifies ITS sequences and extracts the ITS region + +Source code available at: +http://microbiology.se/software/itsx + +Version: 1.0.6 +ITSx -- Identifies ITS sequences and extracts the ITS region +Copyright (C) 2012-2013 Johan Bengtsson-Palme et al. +Contact: Johan Bengtsson-Palme, johan[at]microbiology.se +Programmer: Johan Bengtsson-Palme + +Full installation instructions can be found in the User's Guide. +A quick installation guide follows below. + +ITSx requires Perl and HMMER3. + +1) Perl is usually installed on Unix-like systems by default. If not, it can be retrieved from http://www.perl.org/ + +2) HMMER3 can be found at http://hmmer.janelia.org/software +Download it and follow the on site instructions for installation. + +3) Obtain the ITSx package from http://microbiology.se/software/itsx +Unpack the tarball and move into the newly created "ITSx" directory. + +4) Copy the ITSx file and the ITSx_db directory to your preferred bin directory. + +5) To test if ITSx was successfully installed type "ITSx --help" on the command-line. You should now see the ITSx help message. + +To run ITSx, you need a FASTA-formatted output file. You can e.g. use the test.fasta file supplied with the package. To check for ITS sequences in the test file, type "ITSx -i test.fasta -o test" on the command line. If you are on a multicore machine, you might want to use the "--cpu 2" option to speed up the processes by using two (or more) cores. + +New features in this version: +- Fixed a bug causing over-reporting of chimeras + + +If you encounter a bug or some other strange behaviour, please report it to: +johan[at]microbiology.se + +This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.You should have received a copy of the GNU General Public License along with this program, in a file called 'license.txt'. If not, see: http://www.gnu.org/licenses/. + +---- + +Usage: ITSx -i [input file] -o [output file] + +Options: + +-i {file} : DNA FASTA input file to investigate + +-o {file} : Base for the names of output file(s) + +-p {directory} : A path to a directory of HMM-profile collections representing ITS conserved regions, default is in the same directory as ITSx itself + +--date {T or F} : Adds a date and time stamp to the output directory, off (F) by default + +--reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default + +Sequence selection options: + +-t {character code} : Profile set to use for the search, see the User's Guide (comma-separated), default is all + +-E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5 + +-S {value} : Domain score cutoff for a sequence to be included in the output, default = 0 + +-N {value} : The minimal number of domains that must match a sequence before it is included, default = 2 + +--selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum + +--search_eval {value} : The E-value cutoff used in the HMMER search, high numbers may slow down the process, cannot be used with the --search_score option, default is 0.01 + +--search_score {value} : The score cutoff used in the HMMER search, low numbers may slow down the process, cannot be used with the --search_eval option, default is to used E-value cutoff, not score + +--allow_single_domain {e-value,score or F} : Allow inclusion of sequences that only find a single domain, given that they meet the given E-value and score thresholds, on with parameters 1e-9,0 by default + +--allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default + +--complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default + +--cpu {value} : the number of CPU threads to use, default is 1 + +--multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default + +--heuristics {T or F} : Selects whether to use HMMER's heuristic filtering, off (F) by default + +Output options: + +--summary {T or F} : Summary of results output, on (T) by default + +--graphical {T or F} : 'Graphical' output, on (T) by default + +--fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default + +--preserve {T or F} : Preserve sequence headers in input file instead of printing out ITSx headers, off (F) by default + +--save_regions {SSU,ITS1,5.8S,ITS2,LSU,all,none} : A comma separated list of regions to output separate FASTA files for, 'ITS1,ITS2' by default + +--anchor {integer or HMM} : Saves an additional number of bases before and after each extracted region. If set to 'HMM' all bases matching the corresponding HMM will be output, default = 0 + +--partial {integer} : Saves additional FASTA-files for full and partial ITS sequences longer than the specified cutoff, default = 0 (off) + +--concat {T or F} : Saves a FASTA-file with concatenated ITS sequences (with 5.8S removed), off (F) by default + +--minlen {integer} : Minimum length the ITS regions must be to be outputted in the concatenated file (see above), default = 0 + +--positions {T or F} : Table format output containing the positions ITS sequences were found in, on (T) by default + +--table {T or F} : Table format output of sequences containing probable ITS sequences, off (F) by default + +--not_found {T or F} : Saves a list of non-found entries, on (T) by default + +--detailed_results {T or F} : Saves a tab-separated list of all results, off (F) by default + +--truncate {T or F} : Truncates the FASTA output to only contain the actual ITS sequences found, on (T) by default + +--silent {T or F} : Supresses printing progress info to stderr, off (F) by default + +--graph_scale {value} : Sets the scale of the graph output, if value is zero, a percentage view is shown, default = 0 + +--save_raw {T or F} : Saves all raw data for searches etc. instead of removing it on finish, off (F) by default + +-h : displays this help message + +--help : displays this help message + +--bugs : displays the bug fixes and known bugs in this version of ITSx + +--license : displays licensing information + + </help> + +</tool>