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1 <tool id="cshl_fastx_collapser" name="Collapse">
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2 <description>sequences</description>
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3 <command>
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4 cat '$input' |
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5 fastx_collapser
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6 #if $input.ext == "fastqsanger":
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7 -Q 33
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8 #elif $input.ext == "fastq":
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9 -Q 64
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10 #end if
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11 -v -o '$output'
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12 </command>
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13
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14 <inputs>
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15 <param format="fastq,fastqsanger,fasta" name="input" type="data" label="Library to collapse" />
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16 </inputs>
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17
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18 <tests>
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19 <test>
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20 <param name="input" value="fasta_collapser1.fasta" />
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21 <output name="output" file="fasta_collapser1.out" />
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22 </test>
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23 </tests>
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24
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25 <outputs>
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26 <data format="fasta" name="output" metadata_source="input"
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27 />
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28 </outputs>
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29 <help>
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30
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31 **What it does**
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32
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33 This tool collapses identical sequences in a FASTQ or FASTA file into a single sequence.
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34
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35 --------
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36
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37 **Example**
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38
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39 Example Input File (Sequence "ATAT" appears multiple times)::
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40
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41 >CSHL_2_FC0042AGLLOO_1_1_605_414
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42 TGCG
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43 >CSHL_2_FC0042AGLLOO_1_1_537_759
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44 ATAT
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45 >CSHL_2_FC0042AGLLOO_1_1_774_520
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46 TGGC
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47 >CSHL_2_FC0042AGLLOO_1_1_742_502
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48 ATAT
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49 >CSHL_2_FC0042AGLLOO_1_1_781_514
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50 TGAG
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51 >CSHL_2_FC0042AGLLOO_1_1_757_487
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52 TTCA
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53 >CSHL_2_FC0042AGLLOO_1_1_903_769
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54 ATAT
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55 >CSHL_2_FC0042AGLLOO_1_1_724_499
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56 ATAT
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57
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58 Example Output file::
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59
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60 >1-1
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61 TGCG
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62 >2-4
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63 ATAT
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64 >3-1
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65 TGGC
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66 >4-1
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67 TGAG
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68 >5-1
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69 TTCA
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70
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71 .. class:: infomark
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72
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73 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
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74
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75 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
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76
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77 The following output::
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78
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79 >2-4
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80 ATAT
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81
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82 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
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83
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84 ------
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85
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86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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87
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88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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89
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90 </help>
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91 </tool>
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92 <!-- FASTX-Collapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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