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