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author jjohnson
date Thu, 25 Oct 2012 13:14:50 -0400
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1 <tool id="ribopicker" name="Ribopicker" version="1.0">
2 <description>identify and remove rRNA-like sequences</description>
3 <requirements>
4 </requirements>
5 <command interpreter="perl">
6 ribopicker.pl -f $input -dbs $dbs -id results
7 </command>
8 <inputs>
9 <param name="input" type="data" format="fastq,fasta" label="Input Sequences"/>
10 <param name="dbs" type="select" label="Databases" multiple="true">
11 <!-- from riboPickerConfig.pm -->
12 <option value="rrnadb">rrnadb - Non-redundant Ribosomal RNA Database</option>
13 <option value="slr">slr - SILVA Large subunit reference database (23S/28S)</option>
14 <option value="ssr">ssr - SILVA Small subunit reference database (16S/18S)</option>
15 <option value="test">test - Example test case db</option>
16 </param>
17 <param name="identity" type="integer" optional="true" label=" Alignment identity threshold percentage (1-100)">
18 <help>
19 Alignment identity threshold in percentage (integer from 1-100
20 without %) used to define matching sequences as similar. The
21 identity is calculated for the part of the query sequence that
22 is aligned to a reference sequence. For example, a query
23 sequence of 100 bp that aligns to a reference sequence over the
24 first 50 bp with 40 matching positions has an identity value of
25 80%."
26 </help>
27 <validator type="in_range" message="between 0 and 100" min="1" max="100"/>
28 </param>
29 <param name="coverage" type="integer" optional="true" label="Alignment coverage threshold percentage (1-100)">
30 <help>
31 Alignment coverage threshold in percentage (integer from 1-100
32 without %) used to define matching sequences as similar. The
33 coverage is calculated for the part of the query sequence that
34 is aligned to a reference sequence. For example, a query
35 sequence of 100 bp that aligns to a reference sequence over the
36 first 50 bp with 40 matching positions has an coverage value of
37 50%.
38 </help>
39 <validator type="in_range" message="between 0 and 100" min="1" max="100"/>
40 </param>
41
42 <param name="length" type="integer" optional="true" label="Alignment length threshold">
43 <help>
44 Alignment length threshold used to define matching sequences as
45 similar. For example, a query sequence of 100 bp that aligns to
46 a reference sequence over the first 50 bp with 40 matching
47 positions has an alignment length of 50.
48 </help>
49 <validator type="in_range" message="length needs to be positive" min="1"/>
50 </param>
51
52 <param name="chunk_size" type="integer" optional="true" label="Chunk size of reads in bp as used by BWA-SW (default: 10000000)">
53 <validator type="in_range" message="" min="10000" max="100"/>
54 </param>
55 <param name="z_best" type="integer" optional="true" label="Z-best value as used by BWA-SW (default: 1)">
56 <validator type="in_range" message="" min="1" max="10"/>
57 </param>
58 <param name="score" type="integer" optional="true" label="Alignment score threshold as used by BWA-SW (default: 30)">
59 <validator type="in_range" message="" min="1" max="10"/>
60 </param>
61
62 </inputs>
63 <outputs>
64 <data format_source="input" name="rrna_fa" label="rrna from ${on_string}" from_work_dir="results_rrna.fa">
65 <filter>input.extension.find('fasta') >= 0</filter>
66 </data>
67 <data format_source="input" name="nonrrna_fa" label="non rrna from ${on_string}" from_work_dir="results_nonrrna.fa">
68 <filter>input.extension.find('fasta') >= 0</filter>
69 </data>
70 <data format_source="input" name="rrna_fq" label="rrna from ${on_string}" from_work_dir="results_rrna.fq">
71 <filter>input.extension.find('fastq') >= 0</filter>
72 </data>
73 <data format_source="input" name="nonrrna_fq" label="non rrna from ${on_string}" from_work_dir="results_nonrrna.fq">
74 <filter>input.extension.find('fastq') >= 0</filter>
75 </data>
76 </outputs>
77 <!--
78 <stdio>
79 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
80 <exit_code range="1:" level="fatal" description="Error" />
81 </stdio>
82 -->
83
84 <help>
85
86 <!--
87 Usage:
88 ribopicker [options] -f <file> -dbs <list> ...
89
90 Options:
91 -help | -h
92 Prints the help message and exists.
93
94 -man Prints the full documentation.
95
96 -version
97 Prints the version of the program.
98
99 -show_dbs
100 Prints a list of available databases.
101
102 -f <file>
103 Input file in FASTA or FASTQ format that contains the query
104 sequences.
105
106 -dbs <list>
107 Name of database(s) to use (default: ssr). Names are according
108 to their definition in the config file (riboPickerConfig.pm).
109 Separate multiple database names by comma without spaces.
110
111 Example: -dbs ssr,hmp16s,ncbi16s
112
113 -out_dir <dir>
114 Directory where the results should be written (default: .). If
115 the directory does not exist, it will be created.
116
117 -i <integer>
118 Alignment identity threshold in percentage (integer from 1-100
119 without %) used to define matching sequences as similar. The
120 identity is calculated for the part of the query sequence that
121 is aligned to a reference sequence. For example, a query
122 sequence of 100 bp that aligns to a reference sequence over the
123 first 50 bp with 40 matching positions has an identity value of
124 80%.
125
126 -c <integer>
127 Alignment coverage threshold in percentage (integer from 1-100
128 without %) used to define matching sequences as similar. The
129 coverage is calculated for the part of the query sequence that
130 is aligned to a reference sequence. For example, a query
131 sequence of 100 bp that aligns to a reference sequence over the
132 first 50 bp with 40 matching positions has an coverage value of
133 50%.
134
135 -l <integer>
136 Alignment length threshold used to define matching sequences as
137 similar. For example, a query sequence of 100 bp that aligns to
138 a reference sequence over the first 50 bp with 40 matching
139 positions has an alignment length of 50.
140
141 -no_seq_out
142 Prevents the generation of the fasta/fastq output file for the
143 given coverage and identity thresholds. This feature is e.g.
144 useful for the web-version since -i and -c are set interactively
145 and not yet defined at the data processing step.
146
147 -keep_tmp_files
148 Prevents from unlinking the generated tmp files. These usually
149 include the id file and the .tsv file(s). This feature is e.g.
150 useful for the web-version since .tsv files are used to
151 dynamically generate the output files.
152
153 -id <string>
154 Optional parameter. If not set, ID will be automatically
155 generated to prevent from overwriting previous results. This
156 option is useful if integrated into other tools and the output
157 filenames need to be known. (Use this option to defined the
158 output filename prefix. Output files will end in _rrna.fa and
159 _nonrrna.fa, respectively.)
160
161 -S <integer>
162 Chunk size of reads in bp as used by BWA-SW (default: 10000000).
163
164 -z <integer>
165 Z-best value as used by BWA-SW (default: 1).
166
167 -T <integer>
168 Alignment score threshold as used by BWA-SW (default: 30).
169
170 -->
171
172 </help>
173 </tool>