Mercurial > repos > nml > fasta_extract
comparison fa-extract-sequence.xml @ 0:75e70a6d8d60 draft
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| author | nml |
|---|---|
| date | Mon, 06 Feb 2017 10:27:59 -0500 |
| parents | |
| children | 0470423f5a47 |
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| -1:000000000000 | 0:75e70a6d8d60 |
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| 1 <tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.0.0"> | |
| 2 <description>Extract a single sequence from a fasta file.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="5.18.1">perl</requirement> | |
| 5 <requirement type="package" version="1.6.924">bioperl</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="perl"> | |
| 8 fa-extract-few.pl | |
| 9 -f $dataset | |
| 10 $exact | |
| 11 $inverse | |
| 12 #if $file_or_type.select == "list" | |
| 13 --list $file_or_type.list_file | |
| 14 #else | |
| 15 $file_or_type.id | |
| 16 #end if | |
| 17 | |
| 18 > | |
| 19 $output | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/> | |
| 23 <param name="exact" type="boolean" truevalue="--exact" label="Exact matches only" help="Will only match exact matches for fasta id"/> | |
| 24 <param name="inverse" type="boolean" truevalue="--inverse" label="Entries NOT matching" help="Will return the sequences not matching the given ids"/> | |
| 25 | |
| 26 <conditional name="file_or_type"> | |
| 27 <param name="select" type="select" label="List file or single pattern"> | |
| 28 <option value="list">List file</option> | |
| 29 <option value="single">Single Pattern</option> | |
| 30 </param> | |
| 31 <when value="list"> | |
| 32 <param name="list_file" type="data" format="txt" help="List of pattern to find." label="List file"/> | |
| 33 </when> | |
| 34 <when value="single"> | |
| 35 <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." /> | |
| 36 </when> | |
| 37 </conditional> | |
| 38 | |
| 39 | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 <test> | |
| 46 <output/> | |
| 47 </test> | |
| 48 </tests> | |
| 49 <help> | |
| 50 **Fasta Extract Sequence** | |
| 51 Extracts a fasta sequence from a multfasta by id (exact or partial) | |
| 52 | |
| 53 Latest author: | |
| 54 Written by Philip Mabon - Public Health Agency of Canada | |
| 55 | |
| 56 Original authors: | |
| 57 Written by Torsten Seemann - Victorian Bioinformatics Consortium | |
| 58 | |
| 59 Wrapped by Simon Gladman - Victorian Bioinformatics Consortium | |
| 60 | |
| 61 | |
| 62 ------ | |
| 63 | |
| 64 Outputs in fasta format. | |
| 65 | |
| 66 ------ | |
| 67 | |
| 68 Inputs: | |
| 69 | |
| 70 Fasta dataset | |
| 71 | |
| 72 Sequence id | |
| 73 </help> | |
| 74 <citations> | |
| 75 </citations> | |
| 76 </tool> |