<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>