Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/restrictFromSize.xml @ 36:44d5973c188c
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 15:02:29 -0400 |
| parents | |
| children |
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| 35:d94018ca4ada | 36:44d5973c188c |
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| 1 <tool id="restrictFromSize" name="restrict from size"> | |
| 2 <description>Select the elements of a list of sequences or transcripts with a given size.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'fasta': | |
| 6 -f fasta | |
| 7 #elif $formatType.FormatInputFileName == 'bed': | |
| 8 -f bed | |
| 9 #elif $formatType.FormatInputFileName == 'gff': | |
| 10 -f gff | |
| 11 #elif $formatType.FormatInputFileName == 'gff2': | |
| 12 -f gff2 | |
| 13 #elif $formatType.FormatInputFileName == 'gff3': | |
| 14 -f gff3 | |
| 15 #elif $formatType.FormatInputFileName == 'sam': | |
| 16 -f sam | |
| 17 #elif $formatType.FormatInputFileName == 'gtf': | |
| 18 -f gtf | |
| 19 #end if | |
| 20 | |
| 21 #if $OptionMax.maximum == "Yes": | |
| 22 -M $OptionMax.max | |
| 23 #end if | |
| 24 #if $OptionMin.minimum == "Yes": | |
| 25 -m $OptionMin.min | |
| 26 #end if | |
| 27 | |
| 28 -o $outputFileGff | |
| 29 </command> | |
| 30 | |
| 31 <inputs> | |
| 32 <conditional name="formatType"> | |
| 33 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 34 <option value="fasta">fasta</option> | |
| 35 <option value="bed">bed</option> | |
| 36 <option value="gff">gff</option> | |
| 37 <option value="gff2">gff2</option> | |
| 38 <option value="gff3">gff3</option> | |
| 39 <option value="sam">sam</option> | |
| 40 <option value="gtf">gtf</option> | |
| 41 </param> | |
| 42 <when value="fasta"> | |
| 43 <param name="inputFileName" format="fasta" type="data" label="Input File"/> | |
| 44 </when> | |
| 45 <when value="bed"> | |
| 46 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 47 </when> | |
| 48 <when value="gff"> | |
| 49 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 50 </when> | |
| 51 <when value="gff2"> | |
| 52 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 53 </when> | |
| 54 <when value="gff3"> | |
| 55 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 56 </when> | |
| 57 <when value="sam"> | |
| 58 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
| 59 </when> | |
| 60 <when value="gtf"> | |
| 61 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 62 </when> | |
| 63 </conditional> | |
| 64 | |
| 65 <conditional name="OptionMax"> | |
| 66 <param name="maximum" type="select" label="maximum number of np"> | |
| 67 <option value="Yes">Yes</option> | |
| 68 <option value="No" selected="true">No</option> | |
| 69 </param> | |
| 70 <when value="Yes"> | |
| 71 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
| 72 </when> | |
| 73 <when value="No"> | |
| 74 </when> | |
| 75 </conditional> | |
| 76 | |
| 77 <conditional name="OptionMin"> | |
| 78 <param name="minimum" type="select" label="minimum number of np"> | |
| 79 <option value="Yes">Yes</option> | |
| 80 <option value="No" selected="true">No</option> | |
| 81 </param> | |
| 82 <when value="Yes"> | |
| 83 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> | |
| 84 </when> | |
| 85 <when value="No"> | |
| 86 </when> | |
| 87 </conditional> | |
| 88 | |
| 89 </inputs> | |
| 90 | |
| 91 <outputs> | |
| 92 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/> | |
| 93 </outputs> | |
| 94 | |
| 95 <help> | |
| 96 Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide. | |
| 97 </help> | |
| 98 | |
| 99 </tool> |