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annotate rmap_wrapper.xml @ 1:065a60688a90 draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:29:28 -0400 |
| parents | a0c8173dbdc9 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rmap_wrapper" name="RMAP" version="1.0.0"> |
| 2 <description>for Solexa Short Reads Alignment</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.05">rmap</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 #if $trim.choice=="No": | |
| 8 rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1 | |
| 9 #else: | |
| 10 rmap_wrapper.py $database $input_seq $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"/> | |
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065a60688a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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21 <param name="align_len" type="integer" value="11" label="Minimal length of a hit (-h)" help="seed" /> |
| 0 | 22 <param name="mismatch" type="select" label="Number of mismatches allowed (-m)"> |
| 23 <option value="0">0</option> | |
| 24 <option value="1">1</option> | |
| 25 <option value="3">3</option> | |
| 26 <option value="5">5</option> | |
| 27 </param> | |
| 28 <conditional name="trim"> | |
| 29 <param name="choice" type="select" label="To trim the reads"> | |
| 30 <option value="No">No</option> | |
| 31 <option value="Yes">Yes</option> | |
| 32 </param> | |
| 33 <when value="No"> | |
| 34 </when> | |
| 35 <when value="Yes"> | |
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1
065a60688a90
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
36 <param name="read_len" type="integer" value="36" label="Read length (-w)"/> |
| 0 | 37 </when> |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data name="output1" format="bed"/> | |
| 42 </outputs> | |
| 43 <!-- | |
| 44 <tests> | |
| 45 <test> | |
| 46 <param name="database" value="/galaxy/data/faseq/test" /> | |
| 47 <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/> | |
| 48 <param name="read_len" value="36" /> | |
| 49 <param name="align_len" value="36" /> | |
| 50 <param name="mismatch" value="3" /> | |
| 51 <output name="output1" file="rmap_wrapper_test1.bed"/> | |
| 52 </test> | |
| 53 </tests> | |
| 54 --> | |
| 55 <help> | |
| 56 | |
| 57 .. class:: warningmark | |
| 58 | |
| 59 RMAP was developed for **Solexa** reads. | |
| 60 | |
| 61 .. class:: infomark | |
| 62 | |
| 63 **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. | |
| 64 | |
| 65 ----- | |
| 66 | |
| 67 **What it does** | |
| 68 | |
| 69 This tool runs **rmap** (for more information, please see the reference below), mapping Solexa reads onto a genome build. | |
| 70 | |
| 71 ----- | |
| 72 | |
| 73 **Parameters** | |
| 74 | |
| 75 - *Minimal Length of a Hit* (**-h**) : this is the seed length or the minimal exact match length | |
| 76 - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment | |
| 77 - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end. | |
| 78 | |
| 79 ----- | |
| 80 | |
| 81 **Reference** | |
| 82 | |
| 83 **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/ | |
| 84 | |
| 85 </help> | |
| 86 </tool> |