Mercurial > repos > devteam > rmap
diff rmap_wrapper.xml @ 0:a0c8173dbdc9 draft
Imported from capsule None
author | devteam |
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date | Mon, 19 May 2014 10:59:29 -0400 |
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children | 065a60688a90 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmap_wrapper.xml Mon May 19 10:59:29 2014 -0400 @@ -0,0 +1,86 @@ +<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" size="15" 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" size="15" 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>