[2] | 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 | |
---|
| 73 | This 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> |
---|