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comparison ITSx.xml @ 0:f82c70f54bd7 draft

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author okorol
date Tue, 24 Mar 2015 12:02:48 -0400
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1 <tool id="ITSx" name="ITSx Extractor" version="1.0.6">
2
3 <description>
4 ITSx -- Identifies ITS sequences and extracts the ITS region
5 </description>
6
7 <command interpreter="perl">
8 ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset
9 </command>
10 <requirements>
11 <requirement type="package" version="3.1b1">hmmer</requirement>
12 </requirements>
13 <inputs>
14 <param name="input" type="data" format="fasta" label="Input Fasta"/>
15 <param name="cpu" type="integer" value="1" label="cpu"/>
16 <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Checks both DNA strands against the database"/>
17 <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/>
18 <param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>
19 <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/>
20 </inputs>
21
22 <outputs>
23 <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/>
24 <data name="ITS2" format="fasta" label="Extracted ITS2 Fasta File" from_work_dir="ITSx_out.ITS2.fasta"/>
25 <data name="fullfasta" format="fasta" label="Full Fasta of ITS extracted" from_work_dir="ITSx_out.full.fasta"/>
26 <data name="graph" format="txt" label="Graph of ITS regions" from_work_dir="ITSx_out.graph"/>
27 <data name="nodetect" format="fasta" label="No ITS region" from_work_dir="ITSx_out_no_detections.fasta"/>
28 <data name="positions" format="tabular" label="ITSx feature positions" from_work_dir="ITSx_out.positions.txt"/>
29 <data name="problematic" format="tabular" label="Problematic sequences" from_work_dir="ITSx_out.problematic.txt"/>
30 <data name="summary" format="txt" label="ITSx summary" from_work_dir="ITSx_out.summary.txt"/>
31 <data name="extractions" format="tabular" label="ITSx extraction results" from_work_dir="ITSx_out.extraction.results"/>
32 </outputs>
33
34 <stdio>
35 <regex match="ITSx" source="both" level="log"/>
36 <regex match="analysis" source="both" level="log"/>
37 <regex match="ERROR" source="both" level="fatal"/>
38 <regex match="error" source="both" level="fatal"/>
39 </stdio>
40
41 <test></test>
42 <help>
43 ITSx -- Identifies ITS sequences and extracts the ITS region
44
45 Source code available at:
46 http://microbiology.se/software/itsx
47
48 Version: 1.0.6
49 ITSx -- Identifies ITS sequences and extracts the ITS region
50 Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.
51 Contact: Johan Bengtsson-Palme, johan[at]microbiology.se
52 Programmer: Johan Bengtsson-Palme
53
54 Full installation instructions can be found in the User's Guide.
55 A quick installation guide follows below.
56
57 ITSx requires Perl and HMMER3.
58
59 1) Perl is usually installed on Unix-like systems by default. If not, it can be retrieved from http://www.perl.org/
60
61 2) HMMER3 can be found at http://hmmer.janelia.org/software
62 Download it and follow the on site instructions for installation.
63
64 3) Obtain the ITSx package from http://microbiology.se/software/itsx
65 Unpack the tarball and move into the newly created "ITSx" directory.
66
67 4) Copy the ITSx file and the ITSx_db directory to your preferred bin directory.
68
69 5) To test if ITSx was successfully installed type "ITSx --help" on the command-line. You should now see the ITSx help message.
70
71 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.
72
73 New features in this version:
74 - Fixed a bug causing over-reporting of chimeras
75
76
77 If you encounter a bug or some other strange behaviour, please report it to:
78 johan[at]microbiology.se
79
80 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/.
81
82 ----
83
84 Usage: ITSx -i [input file] -o [output file]
85
86 Options:
87
88 -i {file} : DNA FASTA input file to investigate
89
90 -o {file} : Base for the names of output file(s)
91
92 -p {directory} : A path to a directory of HMM-profile collections representing ITS conserved regions, default is in the same directory as ITSx itself
93
94 --date {T or F} : Adds a date and time stamp to the output directory, off (F) by default
95
96 --reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default
97
98 Sequence selection options:
99
100 -t {character code} : Profile set to use for the search, see the User's Guide (comma-separated), default is all
101
102 -E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5
103
104 -S {value} : Domain score cutoff for a sequence to be included in the output, default = 0
105
106 -N {value} : The minimal number of domains that must match a sequence before it is included, default = 2
107
108 --selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum
109
110 --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
111
112 --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
113
114 --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
115
116 --allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default
117
118 --complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default
119
120 --cpu {value} : the number of CPU threads to use, default is 1
121
122 --multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default
123
124 --heuristics {T or F} : Selects whether to use HMMER's heuristic filtering, off (F) by default
125
126 Output options:
127
128 --summary {T or F} : Summary of results output, on (T) by default
129
130 --graphical {T or F} : 'Graphical' output, on (T) by default
131
132 --fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default
133
134 --preserve {T or F} : Preserve sequence headers in input file instead of printing out ITSx headers, off (F) by default
135
136 --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
137
138 --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
139
140 --partial {integer} : Saves additional FASTA-files for full and partial ITS sequences longer than the specified cutoff, default = 0 (off)
141
142 --concat {T or F} : Saves a FASTA-file with concatenated ITS sequences (with 5.8S removed), off (F) by default
143
144 --minlen {integer} : Minimum length the ITS regions must be to be outputted in the concatenated file (see above), default = 0
145
146 --positions {T or F} : Table format output containing the positions ITS sequences were found in, on (T) by default
147
148 --table {T or F} : Table format output of sequences containing probable ITS sequences, off (F) by default
149
150 --not_found {T or F} : Saves a list of non-found entries, on (T) by default
151
152 --detailed_results {T or F} : Saves a tab-separated list of all results, off (F) by default
153
154 --truncate {T or F} : Truncates the FASTA output to only contain the actual ITS sequences found, on (T) by default
155
156 --silent {T or F} : Supresses printing progress info to stderr, off (F) by default
157
158 --graph_scale {value} : Sets the scale of the graph output, if value is zero, a percentage view is shown, default = 0
159
160 --save_raw {T or F} : Saves all raw data for searches etc. instead of removing it on finish, off (F) by default
161
162 -h : displays this help message
163
164 --help : displays this help message
165
166 --bugs : displays the bug fixes and known bugs in this version of ITSx
167
168 --license : displays licensing information
169
170 </help>
171
172 </tool>