Mercurial > repos > devteam > rmapq
comparison rmapq_wrapper.xml @ 0:f6e5bb5aa2f5 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 19 May 2014 12:34:22 -0400 |
| parents | |
| children | 3a48f010da67 |
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| -1:000000000000 | 0:f6e5bb5aa2f5 |
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| 1 <tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0"> | |
| 2 <description>for Solexa Short Reads Alignment with Quality Scores</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.05">rmap</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 #if $trim.choice=="No": | |
| 8 rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1 | |
| 9 #else: | |
| 10 rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1 | |
| 11 #end if | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param name="database" type="select" display="radio" label="Target database"> | |
| 15 <options from_file="faseq.loc"> | |
| 16 <column name="name" index="0"/> | |
| 17 <column name="value" index="0"/> | |
| 18 </options> | |
| 19 </param> | |
| 20 <param name="input_seq" type="data" format="fasta" label="Sequence file"/> | |
| 21 <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/> | |
| 22 <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/> | |
| 23 <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/> | |
| 24 <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/> | |
| 25 <param name="mismatch" type="select" label="Number of mismatches allowed (-m)"> | |
| 26 <option value="0">0</option> | |
| 27 <option value="1">1</option> | |
| 28 <option value="3">3</option> | |
| 29 <option value="5">5</option> | |
| 30 </param> | |
| 31 <conditional name="trim"> | |
| 32 <param name="choice" type="select" label="To trim the reads"> | |
| 33 <option value="No">No</option> | |
| 34 <option value="Yes">Yes</option> | |
| 35 </param> | |
| 36 <when value="No"> | |
| 37 </when> | |
| 38 <when value="Yes"> | |
| 39 <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)" /> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data name="output1" format="bed"/> | |
| 45 </outputs> | |
| 46 <!-- | |
| 47 <tests> | |
| 48 <test> | |
| 49 <param name="database" value="/galaxy/data/faseq/test" /> | |
| 50 <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/> | |
| 51 <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" /> | |
| 52 <param name="high_score" value="40" /> | |
| 53 <param name="high_len" value="36" /> | |
| 54 <param name="read_len" value="36" /> | |
| 55 <param name="align_len" value="36" /> | |
| 56 <param name="mismatch" value="3" /> | |
| 57 <output name="output1" file="rmapq_wrapper_test1.bed"/> | |
| 58 </test> | |
| 59 </tests> | |
| 60 --> | |
| 61 <help> | |
| 62 | |
| 63 .. class:: warningmark | |
| 64 | |
| 65 RMAPQ was developed for **Solexa** reads. | |
| 66 | |
| 67 .. class:: infomark | |
| 68 | |
| 69 **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. | |
| 70 | |
| 71 ----- | |
| 72 | |
| 73 **What it does** | |
| 74 | |
| 75 This tool runs **rmapq** (for more information, please see the reference below), searching against a genome build with sequence qualities. | |
| 76 | |
| 77 ----- | |
| 78 | |
| 79 **Parameters** | |
| 80 | |
| 81 - *Minimal High-quality Bases* (**-M**): the minimal length of the high quality score bases | |
| 82 - *Minimum Score for High-quality Base* (**-q**) : the minimal quality score | |
| 83 - *Minimal Length of a Hit* (**-h**) : the minimal length of an exact match or seed | |
| 84 - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment | |
| 85 - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end. | |
| 86 | |
| 87 ----- | |
| 88 | |
| 89 **Reference** | |
| 90 | |
| 91 **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/ | |
| 92 | |
| 93 </help> | |
| 94 </tool> |