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author | devteam |
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date | Tue, 13 Oct 2015 12:29:28 -0400 |
parents | a0c8173dbdc9 |
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<tool id="rmap_wrapper" name="RMAP" version="1.0.0"> <description>for Solexa Short Reads Alignment</description> <requirements> <requirement type="package" version="2.05">rmap</requirement> </requirements> <command interpreter="python"> #if $trim.choice=="No": rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1 #else: rmap_wrapper.py $database $input_seq $trim.read_len $align_len $mismatch $output1 #end if </command> <inputs> <param name="database" type="select" display="radio" label="Target database"> <options from_file="faseq.loc"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="input_seq" type="data" format="fasta" label="Sequence file"/> <param name="align_len" type="integer" value="11" label="Minimal length of a hit (-h)" help="seed" /> <param name="mismatch" type="select" label="Number of mismatches allowed (-m)"> <option value="0">0</option> <option value="1">1</option> <option value="3">3</option> <option value="5">5</option> </param> <conditional name="trim"> <param name="choice" type="select" label="To trim the reads"> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="No"> </when> <when value="Yes"> <param name="read_len" type="integer" value="36" label="Read length (-w)"/> </when> </conditional> </inputs> <outputs> <data name="output1" format="bed"/> </outputs> <!-- <tests> <test> <param name="database" value="/galaxy/data/faseq/test" /> <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/> <param name="read_len" value="36" /> <param name="align_len" value="36" /> <param name="mismatch" value="3" /> <output name="output1" file="rmap_wrapper_test1.bed"/> </test> </tests> --> <help> .. class:: warningmark RMAP was developed for **Solexa** reads. .. class:: infomark **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. ----- **What it does** This tool runs **rmap** (for more information, please see the reference below), mapping Solexa reads onto a genome build. ----- **Parameters** - *Minimal Length of a Hit* (**-h**) : this is the seed length or the minimal exact match length - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end. ----- **Reference** **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/ </help> </tool>