Mercurial > repos > drosofff > msp_fasta_tabular_converter
comparison fasta_tabular_converter.xml @ 0:951cb6b3979b draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Sun, 21 Jun 2015 14:28:49 -0400 |
| parents | |
| children | 2f7278120be9 |
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| -1:000000000000 | 0:951cb6b3979b |
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| 1 <tool id="fasta_tabular_converter" name="fasta - tabular" version="1.0.2"> | |
| 2 <description>conversions</description> | |
| 3 <command interpreter="python">fasta_tabular_converter.py $input $output $switch.conversionType</command> | |
| 4 <inputs> | |
| 5 <conditional name="switch"> | |
| 6 <param name="conversionType" type="select" label="conversion option"> | |
| 7 <option value="fasta2tabular" selected="true">fasta to tabular</option> | |
| 8 <option value="tabular2fasta">tabular to fasta</option> | |
| 9 <option value="tabular2fastaweight">tabular to weighted fasta</option> | |
| 10 <option value="fastaweight2fastaweight">recompile weighted fasta to catenated fasta weighted</option> | |
| 11 <option value="fastaweight2fasta">fasta weighted to fasta</option> | |
| 12 </param> | |
| 13 <when value="fasta2tabular"> | |
| 14 <param name="input" type="data" format="fasta" label="fasta file to convert to tabular"/> | |
| 15 </when> | |
| 16 <when value="tabular2fasta"> | |
| 17 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta"/> | |
| 18 </when> | |
| 19 <when value="tabular2fastaweight"> | |
| 20 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta weighted"/> | |
| 21 </when> | |
| 22 <when value="fastaweight2fastaweight"> | |
| 23 <param name="input" type="data" format="fasta" label="catenated fasta weighted to recompile" help="Use this option only if you known what you're doing"/> | |
| 24 </when> | |
| 25 <when value="fastaweight2fasta"> | |
| 26 <param name="input" type="data" format="fasta" label="fasta weighted file to convert to fasta"/> | |
| 27 </when> | |
| 28 </conditional> | |
| 29 | |
| 30 </inputs> | |
| 31 | |
| 32 <outputs> | |
| 33 <data format="fasta" name="output" label="${switch.conversionType} conversion"> | |
| 34 <change_format> | |
| 35 <when input="switch.conversionType" value="fasta2tabular" format="tabular"/> | |
| 36 <when input="switch.conversionType" value="fastaweight2fastaweight" format="fasta"/> | |
| 37 <when input="switch.conversionType" value="fastaweight2fasta" format="fasta"/> | |
| 38 </change_format> | |
| 39 </data> | |
| 40 </outputs> | |
| 41 | |
| 42 <tests> | |
| 43 <test> | |
| 44 <param name="conversionType" value="fasta2tabular" /> | |
| 45 <param ftype="fasta" name="input" value="input.fa" /> | |
| 46 <output file="output.tab" name="output" /> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="conversionType" value="tabular2fastaweight" /> | |
| 50 <param ftype="tabular" name="input" value="output.tab" /> | |
| 51 <output file="output.faw" name="output" /> | |
| 52 </test> | |
| 53 </tests> | |
| 54 | |
| 55 | |
| 56 <help> | |
| 57 | |
| 58 **What it does** | |
| 59 | |
| 60 Converts fasta files to tabular files with sequence on first column and occurence of the sequence in the second column; and reciprocally. | |
| 61 | |
| 62 This format is suitable for storage of sequence datasets in the data library, and will be used in the future. | |
| 63 | |
| 64 Regeneration of the original fasta file from the tabular format is ensured by the same tool | |
| 65 | |
| 66 This tool also handle a fasta "weigthed" format with headers as: | |
| 67 >id_numberofreads | |
| 68 ATGCATGACCAGATAGGAC | |
| 69 etc... | |
| 70 | |
| 71 with generation of the "weigthed" format from a tabular format, and recompilation of catenated weighted fasta files | |
| 72 | |
| 73 </help> | |
| 74 | |
| 75 </tool> |