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annotate fastx_collapser.xml @ 2:17bfc147c9ea draft

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author devteam
date Tue, 13 Oct 2015 12:41:05 -0400
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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>
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7 <![CDATA[
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8 zcat -f < '$input' | fastx_collapser -v -o '$output'
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9 #if $input.ext == "fastqsanger":
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10 -Q 33
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11 #end if
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12 ]]>
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13 </command>
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14
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15 <inputs>
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16 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
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17 </inputs>
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18 <outputs>
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19 <data format="fasta" name="output" metadata_source="input" />
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20 </outputs>
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21 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
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22 <tests>
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23 <test>
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24 <param name="input" value="fasta_collapser1.fasta" />
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25 <param name="output" file="fasta_collapser1.out" />
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26 </test>
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27 </tests>
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28 -->
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29 <help>
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30 **What it does**
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31
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32 This tool collapses identical sequences in a FASTA file into a single sequence.
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33
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34 --------
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35
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36 **Example**
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37
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38 Example Input File (Sequence "ATAT" appears multiple times)::
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39
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40 >CSHL_2_FC0042AGLLOO_1_1_605_414
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41 TGCG
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42 >CSHL_2_FC0042AGLLOO_1_1_537_759
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43 ATAT
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44 >CSHL_2_FC0042AGLLOO_1_1_774_520
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45 TGGC
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46 >CSHL_2_FC0042AGLLOO_1_1_742_502
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47 ATAT
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48 >CSHL_2_FC0042AGLLOO_1_1_781_514
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49 TGAG
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50 >CSHL_2_FC0042AGLLOO_1_1_757_487
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51 TTCA
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52 >CSHL_2_FC0042AGLLOO_1_1_903_769
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53 ATAT
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54 >CSHL_2_FC0042AGLLOO_1_1_724_499
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55 ATAT
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56
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57 Example Output file::
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58
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59 >1-1
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60 TGCG
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61 >2-4
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62 ATAT
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63 >3-1
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64 TGGC
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65 >4-1
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66 TGAG
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67 >5-1
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68 TTCA
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69
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70 .. class:: infomark
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71
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72 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
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73
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74 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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75
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76 The following output::
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77
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78 >2-4
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79 ATAT
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80
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81 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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82
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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 </help>
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90 </tool>