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1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
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2 <description>sequences</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>zcat -f '$input' | fastx_collapser -v -o '$output'
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7 #if $input.ext == "fastqsanger":
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8 -Q 33
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9 #end if
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10 </command>
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11
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12 <inputs>
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13 <param format="fasta,fastqsanger,fastqsolexa" version="1.0.0" name="input" type="data" label="Library to collapse" />
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14 </inputs>
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15
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16 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
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17 <tests>
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18 <test>
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19 <param version="1.0.0" name="input" value="fasta_collapser1.fasta" />
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20 <output version="1.0.0" name="output" file="fasta_collapser1.out" />
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21 </test>
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22 </tests>
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23 -->
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24 <outputs>
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25 <data format="fasta" version="1.0.0" name="output" metadata_source="input" />
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26 </outputs>
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27 <help>
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28
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29 **What it does**
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30
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31 This tool collapses identical sequences in a FASTA file into a single sequence.
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32
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33 --------
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34
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35 **Example**
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36
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37 Example Input File (Sequence "ATAT" appears multiple times)::
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38
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39 >CSHL_2_FC0042AGLLOO_1_1_605_414
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40 TGCG
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41 >CSHL_2_FC0042AGLLOO_1_1_537_759
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42 ATAT
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43 >CSHL_2_FC0042AGLLOO_1_1_774_520
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44 TGGC
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45 >CSHL_2_FC0042AGLLOO_1_1_742_502
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46 ATAT
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47 >CSHL_2_FC0042AGLLOO_1_1_781_514
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48 TGAG
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49 >CSHL_2_FC0042AGLLOO_1_1_757_487
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50 TTCA
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51 >CSHL_2_FC0042AGLLOO_1_1_903_769
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52 ATAT
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53 >CSHL_2_FC0042AGLLOO_1_1_724_499
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54 ATAT
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55
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56 Example Output file::
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57
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58 >1-1
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59 TGCG
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60 >2-4
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61 ATAT
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62 >3-1
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63 TGGC
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64 >4-1
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65 TGAG
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66 >5-1
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67 TTCA
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68
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69 .. class:: infomark
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70
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71 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
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72
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73 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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74
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75 The following output::
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76
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77 >2-4
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78 ATAT
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79
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80 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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81
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82
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83 ------
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84
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85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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86
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87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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88
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89 </help>
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90 </tool>
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