Mercurial > repos > bgruening > find_subsequences
comparison find_subsequences.xml @ 0:9bc84bbab418 draft
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| author | bgruening |
|---|---|
| date | Thu, 19 Mar 2015 09:40:43 -0400 |
| parents | |
| children | decaf3f8fec9 |
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| -1:000000000000 | 0:9bc84bbab418 |
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| 1 <tool id="bg_find_subsequences" name="Subsequence search" version="0.1"> | |
| 2 <description>providing regions in BED format</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.6.5">biopyhon</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 <![CDATA[ | |
| 8 find_subsequences.py | |
| 9 --input $input | |
| 10 --output $output | |
| 11 --pattern "$pattern" | |
| 12 #if $input.ext == 'fasta': | |
| 13 --format 'fasta' | |
| 14 #else: | |
| 15 --format 'fastq' | |
| 16 #end if | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="fasta,fastq" name="input" type="data" label="Sequence to be searched" | |
| 21 help="This can be in FASTA or FASTQ format." /> | |
| 22 <param name="pattern" type="text" value="" label="Search pattern" help="For example GGATCC for BamH1."> | |
| 23 <validator type="regex" message="Only letters are allowed.">^[a-zA-Z]+$</validator> | |
| 24 </param> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="bed" name="output" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> | |
| 32 <param name="pattern" value="atcg"/> | |
| 33 <output name="output" file="find_subsequences_simple_result1.bed" ftype="bed"/> | |
| 34 </test> | |
| 35 <test> | |
| 36 <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> | |
| 37 <param name="pattern" value="atnncg"/> | |
| 38 <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help> | |
| 42 <![CDATA[ | |
| 43 | |
| 44 **What it does** | |
| 45 | |
| 46 Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamH1. | |
| 47 | |
| 48 If you are searching in a DNA sequence you can use ambiguous values using the standard | |
| 49 `nucleotide ambiguity code <http://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html>`_. | |
| 50 | |
| 51 This tool is searching on both strands. | |
| 52 | |
| 53 ]]> | |
| 54 </help> | |
| 55 <citations> | |
| 56 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
| 57 </citations> | |
| 58 </tool> |