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/tools/metag_tools/rmap_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="rmap_wrapper" name="RMAP" version="1.0.0">
 2    <description>for Solexa Short Reads Alignment</description>
 3    <command interpreter="python">
 4    #if $trim.choice=="No": #rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1
 5    #else: #rmap_wrapper.py $database $input_seq $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="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed" />
17        <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
18            <option value="0">0</option>
19            <option value="1">1</option>
20            <option value="3">3</option>
21            <option value="5">5</option>
22        </param>
23        <conditional name="trim">
24            <param name="choice" type="select" label="To trim the reads">
25                <option value="No">No</option>
26                <option value="Yes">Yes</option>
27            </param>
28            <when value="No">
29            </when>
30            <when value="Yes">
31                <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)"/> 
32            </when>
33        </conditional>
34    </inputs>
35    <outputs>
36        <data name="output1" format="bed"/>
37    </outputs>
38    <requirements>
39      <requirement type="binary">rmap</requirement>
40    </requirements>
41    <!--     
42    <tests>
43        <test>
44            <param name="database" value="/galaxy/data/faseq/test" />
45            <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/>
46            <param name="read_len" value="36" />
47            <param name="align_len" value="36" />
48            <param name="mismatch" value="3" />
49            <output name="output1" file="rmap_wrapper_test1.bed"/> 
50        </test>
51    </tests>
52     -->
53    <help>
54    
55.. class:: warningmark
56
57 RMAP was developed for **Solexa** reads. 
58
59.. class:: infomark
60
61**TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Reads length* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end. 
62
63-----
64
65**What it does**
66
67This tool runs **rmap** (for more information, please see the reference below), mapping Solexa reads onto a genome build.   
68
69-----
70
71**Parameters**
72
73- *Minimal Length of a Hit* (**-h**) : this is the seed length or the minimal exact match length   
74- *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment 
75- *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.
76
77-----
78
79**Reference**
80
81 **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/
82
83    </help>
84</tool>