[2] | 1 | <tool id="rmap_wrapper" name="RMAP" version="1.0.0"> |
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| 2 | <description>for Solexa Short Reads Alignment</description> |
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| 3 | <command interpreter="python"> |
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| 4 | #if $trim.choice=="No": #rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1 |
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| 5 | #else: #rmap_wrapper.py $database $input_seq $trim.read_len $align_len $mismatch $output1 |
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| 6 | #end if |
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| 7 | </command> |
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| 8 | <inputs> |
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| 9 | <param name="database" type="select" display="radio" label="Target database"> |
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| 10 | <options from_file="faseq.loc"> |
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| 11 | <column name="name" index="0"/> |
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| 12 | <column name="value" index="0"/> |
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| 13 | </options> |
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| 14 | </param> |
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| 15 | <param name="input_seq" type="data" format="fasta" label="Sequence file"/> |
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| 16 | <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed" /> |
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| 17 | <param name="mismatch" type="select" label="Number of mismatches allowed (-m)"> |
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| 18 | <option value="0">0</option> |
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| 19 | <option value="1">1</option> |
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| 20 | <option value="3">3</option> |
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| 21 | <option value="5">5</option> |
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| 22 | </param> |
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| 23 | <conditional name="trim"> |
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| 24 | <param name="choice" type="select" label="To trim the reads"> |
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| 25 | <option value="No">No</option> |
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| 26 | <option value="Yes">Yes</option> |
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| 27 | </param> |
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| 28 | <when value="No"> |
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| 29 | </when> |
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| 30 | <when value="Yes"> |
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| 31 | <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)"/> |
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| 32 | </when> |
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| 33 | </conditional> |
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| 34 | </inputs> |
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| 35 | <outputs> |
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| 36 | <data name="output1" format="bed"/> |
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| 37 | </outputs> |
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| 38 | <requirements> |
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| 39 | <requirement type="binary">rmap</requirement> |
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| 40 | </requirements> |
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| 41 | <!-- |
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| 42 | <tests> |
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| 43 | <test> |
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| 44 | <param name="database" value="/galaxy/data/faseq/test" /> |
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| 45 | <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/> |
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| 46 | <param name="read_len" value="36" /> |
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| 47 | <param name="align_len" value="36" /> |
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| 48 | <param name="mismatch" value="3" /> |
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| 49 | <output name="output1" file="rmap_wrapper_test1.bed"/> |
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| 50 | </test> |
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| 51 | </tests> |
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| 52 | --> |
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| 53 | <help> |
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| 54 | |
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| 55 | .. class:: warningmark |
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| 56 | |
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| 57 | RMAP was developed for **Solexa** reads. |
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| 58 | |
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| 59 | .. class:: infomark |
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| 60 | |
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| 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. |
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| 62 | |
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| 63 | ----- |
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| 64 | |
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| 65 | **What it does** |
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| 66 | |
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| 67 | This tool runs **rmap** (for more information, please see the reference below), mapping Solexa reads onto a genome build. |
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| 68 | |
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| 69 | ----- |
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| 70 | |
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| 71 | **Parameters** |
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| 72 | |
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| 73 | - *Minimal Length of a Hit* (**-h**) : this is the seed length or the minimal exact match length |
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| 74 | - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment |
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| 75 | - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end. |
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| 76 | |
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| 77 | ----- |
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| 78 | |
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| 79 | **Reference** |
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| 80 | |
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| 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/ |
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| 82 | |
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| 83 | </help> |
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| 84 | </tool> |
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