Mercurial > repos > yufei-luo > s_mart
comparison SMART/bacteriaRegulatoryRegion_Detection/changeName.xml @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
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| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 <tool id="changeName" name="changeName"> | |
| 2 <description>Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.</description> | |
| 3 <command interpreter="python"> | |
| 4 changeName.py | |
| 5 #if $optionFasta.fastaFile == 'Yes': | |
| 6 --input1 $optionFasta.fasta --output1 $outputFasta | |
| 7 #end if | |
| 8 #if $optionGff.gffFile == 'Yes': | |
| 9 --input2 $optionGff.gff --output2 $outputGff | |
| 10 #end if | |
| 11 #if $optionSam.samFile == 'Yes': | |
| 12 --input3 $optionSam.sam --output3 $outputSam | |
| 13 #end if | |
| 14 #if $optionName.name == 'Yes': | |
| 15 --name $optionName.nameValue | |
| 16 #end if | |
| 17 </command> | |
| 18 | |
| 19 <inputs> | |
| 20 <conditional name="optionFasta"> | |
| 21 <param name="fastaFile" type="select" label="You can choose a fasta input file to change the name." > | |
| 22 <option value="Yes">Yes</option> | |
| 23 <option value="No" selected="true">No</option> | |
| 24 </param> | |
| 25 <when value="Yes"> | |
| 26 <param name="fasta" format="fasta" type="data" label="Identify you fasta input file."/> | |
| 27 </when> | |
| 28 <when value="No"> | |
| 29 </when> | |
| 30 </conditional> | |
| 31 | |
| 32 <conditional name="optionGff"> | |
| 33 <param name="gffFile" type="select" label="You can choose a supplementary gff input file to change the name." > | |
| 34 <option value="Yes">Yes</option> | |
| 35 <option value="No" selected="true">No</option> | |
| 36 </param> | |
| 37 <when value="Yes"> | |
| 38 <param name="gff" format="gff" type="data" label="Identify you gff input file."/> | |
| 39 </when> | |
| 40 <when value="No"> | |
| 41 </when> | |
| 42 </conditional> | |
| 43 | |
| 44 <conditional name="optionSam"> | |
| 45 <param name="samFile" type="select" label="You can choose a supplementary sam input file to change the name." > | |
| 46 <option value="Yes">Yes</option> | |
| 47 <option value="No" selected="true">No</option> | |
| 48 </param> | |
| 49 <when value="Yes"> | |
| 50 <param name="sam" format="sam" type="data" label="Identify you sam input file."/> | |
| 51 </when> | |
| 52 <when value="No"> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 | |
| 56 <conditional name="optionName"> | |
| 57 <param name="name" type="select" label="Identify a new name to change." > | |
| 58 <option value="Yes">Yes</option> | |
| 59 <option value="No" selected="true">No</option> | |
| 60 </param> | |
| 61 <when value="Yes"> | |
| 62 <param name="nameValue" type="text" value="None" label="Identify the new name."/> | |
| 63 </when> | |
| 64 <when value="No"> | |
| 65 </when> | |
| 66 </conditional> | |
| 67 </inputs> | |
| 68 | |
| 69 <outputs> | |
| 70 <data name="outputFasta" format="fasta"> | |
| 71 <filter>optionFasta['fastaFile'] == 'Yes'</filter> | |
| 72 </data> | |
| 73 <data format="gff" name="outputGff" > | |
| 74 <filter>optionGff['gffFile'] == 'Yes'</filter> | |
| 75 </data> | |
| 76 <data format="sam" name="outputSam" > | |
| 77 <filter>optionSam['samFile'] == 'Yes'</filter> | |
| 78 </data> | |
| 79 </outputs> | |
| 80 </tool> |