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comparison snpsplit.xml @ 4:bd5692103d5b draft

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author rreumerman
date Fri, 05 Apr 2013 05:00:40 -0400
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3:a808647d7312 4:bd5692103d5b
1 <tool id="snpsplit" name="SNP splitter">
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3 <description>splits multicharacter entries into separate lines</description>
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5 <command interpreter="python">snpsplit.py $input $output</command>
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7 <inputs>
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9 <param name="input" type="data" format="tabular" label="SNP table" />
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11 </inputs>
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13 <outputs>
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15 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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17 </outputs>
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19 <help>
20
21
22 **What it does**
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26 SNPsplit prepares tab-delimited SNP files for TRAMS. It checks each line for entries that contain multiple consecutive bases and splits them over several lines.
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30 - **Input**: tab delimited, format: Position Ref Pol
31 - Position is 1-based genomic coordinate
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33 - Ref is the reference sequence
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35 - Pol is the polymorphism sequence
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39 Ref en Mut sequences consisting of more than one character will be split up into separate lines. Example:
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43 **Input**:
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45
46 === === ===
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48 123 CGT ATG
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50 === === ===
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52
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54 **Output**:
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57 === = =
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59 123 C A
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61 124 G T
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63 125 T G
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65 === = =
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69 Bases that are the same in both columns, will be skipped. Example:
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73 **Input**:
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75
76 === ===== ===
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78 123 C*G*T AGG
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80 === ===== ===
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82
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84 **Output**:
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86
87 === = =
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89 123 C A
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91 125 T G
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93 === = =
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96 </help>
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98 </tool>