/tools/metag_tools/rmapq_wrapper.xml

 1<tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0">
 2    <description>for Solexa Short Reads Alignment with Quality Scores</description>
 3    <command interpreter="python">
 4    #if $trim.choice=="No": #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1
 5    #else: #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1
 6    #end if
 7    </command>
 8    <inputs>
 9        <param name="database" type="select" display="radio" label="Target database">
10			<options from_file="faseq.loc">
11			  <column name="name" index="0"/>
12			  <column name="value" index="0"/>
13			</options>
14        </param>
15        <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
16        <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
17        <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
18        <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
19        <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
20        <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
21            <option value="0">0</option>
22            <option value="1">1</option>
23            <option value="3">3</option>
24            <option value="5">5</option>
25        </param>
26        <conditional name="trim">
27            <param name="choice" type="select" label="To trim the reads">
28                <option value="No">No</option>
29                <option value="Yes">Yes</option>
30            </param>
31            <when value="No">
32            </when>
33            <when value="Yes">
34                <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)" /> 
35            </when>
36        </conditional>
37    </inputs>
38    <outputs>
39        <data name="output1" format="bed"/>
40    </outputs>
41    <requirements>
42      <requirement type="binary">rmapq</requirement>
43    </requirements>
44    <!-- 
45    <tests>
46        <test>
47            <param name="database" value="/galaxy/data/faseq/test" />
48            <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
49            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
50            <param name="high_score" value="40" />
51            <param name="high_len" value="36" />
52            <param name="read_len" value="36" />
53            <param name="align_len" value="36" />
54            <param name="mismatch" value="3" />
55            <output name="output1" file="rmapq_wrapper_test1.bed"/> 
56        </test>
57    </tests>
58    -->
59    <help>
60    
61.. class:: warningmark
62
63 RMAPQ was developed for **Solexa** reads. 
64
65.. class:: infomark
66
67**TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Maximal Length of the Reads* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end. 
68
69-----
70
71**What it does**
72
73This tool runs **rmapq** (for more information, please see the reference below), searching against a genome build with sequence qualities.   
74
75-----
76
77**Parameters**
78
79- *Minimal High-quality Bases* (**-M**): the minimal length of the high quality score bases
80- *Minimum Score for High-quality Base* (**-q**) : the minimal quality score 
81- *Minimal Length of a Hit* (**-h**) : the minimal length of an exact match or seed  
82- *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment
83- *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.
84
85-----
86
87**Reference**
88
89 **RMAP** is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/
90
91    </help>
92</tool>