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1 <?xml version="1.0"?>
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2 <tool id="clean_fasta_header_1" name="Clean fasta header">
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3 <description>Removes fasta description fields in header </description>
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4 <command>sed 's/\(>\w*\)\s*.*/\1/' $inputFastaFile > $fasta_outputfile</command>
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5 <inputs>
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6 <param format="fasta" name="inputFastaFile" type="data" label="fasta File"/>
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7 </inputs>
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8 <outputs>
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9 <data format="fasta" name="fasta_outputfile" />
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10 </outputs>
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11 <help>
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12 .. class:: infomark
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13
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14 **TIP**
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15
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16 This tool requires *fasta* format.
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17
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18 It simply removes any additional definition strings from the header line prior to using tools that dont handle these.
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19
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20 ----
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21
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22 **Example**
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23
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24 --Query sequence
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25
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26 ::
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27
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28 >contig00001 gene=isogroup00001 length=2159
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29 tttAaGCATTTAACACTGCATATTGATTGATATAGTTGTTCAGTACAAGCCAATTACATT
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30 GTAGACATAAAACAAAGCATTCGAAACAGTTGAAATTTTGATTCCTCTATACTGGATCAG
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31 GCGGTAATCA
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32 >contig00003 gene=isogroup00001 length=2206
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33 ggTGGCTGCTTTCTCAAATCCACCCCTTCCCAAGGAAACCCTAAACTCGCAGATAAATTT
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34
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35
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36
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37 --Output
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38
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39 ::
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40
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41 >contig00001
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42 ttAaGCATTTAACACTGCATATTGATTGATATAGTTGTTCAGTACAAGCCAATTACATT
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43 GTAGACATAAAACAAAGCATTCGAAACAGTTGAAATTTTGATTCCTCTATACTGGATCAG
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44 GCGGTAATCAGGGGAAGGAAACCATGGTGTAAGGCTGCATCCCATACTTTATCTATGTCA
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45 >contig00003
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46 ggTGGCTGCTTTCTCAAATCCACCCCTTCCCAAGGAAACCCTAAACTCGCAGATAAATTT
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47 GTAGGGTTTCTATGTCGACCGAGCGCCGTCGGAAAGTGAGCCTTTTCGACGTAGTTGAC
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48 GAGACCTCAGTCTCTG...
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49
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50
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51 </help>
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52
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53 </tool>
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