annotate uclust2otutable.xml @ 0:e85e7ba38aff draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
author qfabrepo
date Mon, 14 Sep 2020 04:52:36 +0000 (2020-09-14)
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children 046085ec595c
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e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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1 <tool id="uclust2otutable" name="OTUTable" version="1.0.0">
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2 <description>Convert UCLUST format from Vsearch to OTU Table</description>
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3 <version_command>
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4 python ${__tool_directory__}/uclust2otutable.py --version
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5 </version_command>
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6 <command detect_errors="aggressive">
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7 python ${__tool_directory__}/uclust2otutable.py
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8 -i '$inputfile'
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9 -o '$output'
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10 </command>
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11 <inputs>
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12 <param format="tabular" name="inputfile" type="data" label="UCLUST from Vsearch" />
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13 </inputs>
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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14 <outputs>
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15 <data format="tabular" name="output" label="OTU_TABLE_${inputfile.display_name}"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="inputfile" value="uc_input.txt"/>
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20 <output name="output" file="uc_output.txt"/>
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21 </test>
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22 </tests>
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23
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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24 <help>
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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25 ** what it does **
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26
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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27 Converts UCLUST format (.uc) output from Vsearch search into raw count table. The description of UCLUST format is based on the information that can be found on UCLUST_ documentation page.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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28
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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29 .. _UCLUST: http://www.drive5.com/uclust/uclust_userguide_1_1_579.html
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30
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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31 --------
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32
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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33 =======
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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34 Example
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35 =======
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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36
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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37 Some example records:
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38 ---------------------
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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39
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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40 ==== ======= ==== ==== ====== === === ========= ========== ======
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41 Type Cluster Size %Id Strand Qlo Tlo Alignment Query Target
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42 ---- ------- ---- ---- ------ --- --- --------- ---------- ------
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43 S 0 292 '*' '*' '*' '*' '*' AH70_12410 '*'
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44 H 0 292 99.7 '+' 0 0 292M AH70_12410 '*'
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45 S 0 292 '*' '*' '*' '*' '*' AH70_12410 '*'
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46 H 0 292 98.2 '+' 0 0 292M AH70_12410 '*'
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47 ==== ======= ==== ==== ====== === === ========= ========== ======
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48
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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49 Each record has ten fields, separated by tabs:
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50 ----------------------------------------------
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51
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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52 ========= ===========================================
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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53 Column Description
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54 --------- -------------------------------------------
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55 Type Record type
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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56 Cluster Cluster number
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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57 Size Sequence length or cluster size
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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58 %Id Identity to the seed(as a percentage), or * if this is a seed.
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59 Strand '+' plus strand, '-' minus strand, or '.' amino acids.
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60 Qlo 0-based coordinate of alignment start in the query sequence.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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61 Tlo 0-based coordinate of alignment start in target (seed) sequence. If minus strand, Tlo is relative to start of reverse-complement target.
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62 Alignment Compressed representation of alignment to the seed(see below), or '*' if a seed.
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63 Query FASTA label of query sequence
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64 Target FASTA label of target(seed / library / database) sequence. or '*' if a seed.
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65 ========= ===========================================
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66
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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67 Record Types are:
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68 -----------------
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69
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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70 ====== ===========================================
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71 Column Description
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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72 ------ -------------------------------------------
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73 L Library seed(generated only if a match if found to this seed).
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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74 S New seed.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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75 H Hit, also known as an accept; i.e. a successful match.
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76 D Library cluster.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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77 C New cluster.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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78 N Not matched (a sequence that didn't match library with --libonly specified).
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79 R Reject (generated only if --output_rejects is specified)
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80 ====== ===========================================
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81
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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82 The alignment is compressed using run-length encoding, as follows. Each column in the alignment is classified as M,D or I:
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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83 --------------------------------------------------------------------------------------------------------------------------
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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84
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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85 ==== ====== ============== =============
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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86 Code Name Query sequence Seed sequence
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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87 ---- ------ -------------- -------------
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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88 M Match Letter Letter
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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89 D Delete Gap Letter
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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90 I Insert Letter Gap
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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91 ==== ====== ============== =============
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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92
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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93 --------
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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94
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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95
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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96 </help>
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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97
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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98 </tool>