annotate uclust2otutable.xml @ 1:046085ec595c draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit b67df82f2bd8af214bba5184e9eab4f187b7a4a6"
author qfabrepo
date Wed, 16 Sep 2020 09:27:00 +0000
parents e85e7ba38aff
children 08ca35e99b74
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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 <requirements>
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4 <requirement type="package" version="1.3">progress</requirement>
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5 </requirements>
0
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6 <version_command>
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7 python ${__tool_directory__}/uclust2otutable.py --version
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8 </version_command>
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9 <command detect_errors="aggressive">
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10 python ${__tool_directory__}/uclust2otutable.py
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11 -i '$inputfile'
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12 -o '$output'
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13 </command>
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14 <inputs>
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15 <param format="tabular" name="inputfile" type="data" label="UCLUST from Vsearch" />
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="output" label="OTU_TABLE_${inputfile.display_name}"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="inputfile" value="uc_input.txt"/>
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23 <output name="output" file="uc_output.txt"/>
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24 </test>
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25 </tests>
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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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27 <help>
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28 ** what it does **
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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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30 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.
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32 .. _UCLUST: http://www.drive5.com/uclust/uclust_userguide_1_1_579.html
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33
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34 --------
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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 Example
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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 Some example records:
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41 ---------------------
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42
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43 ==== ======= ==== ==== ====== === === ========= ========== ======
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44 Type Cluster Size %Id Strand Qlo Tlo Alignment Query Target
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45 ---- ------- ---- ---- ------ --- --- --------- ---------- ------
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46 S 0 292 '*' '*' '*' '*' '*' AH70_12410 '*'
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47 H 0 292 99.7 '+' 0 0 292M AH70_12410 '*'
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48 S 0 292 '*' '*' '*' '*' '*' AH70_12410 '*'
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49 H 0 292 98.2 '+' 0 0 292M AH70_12410 '*'
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50 ==== ======= ==== ==== ====== === === ========= ========== ======
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51
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52 Each record has ten fields, separated by tabs:
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53 ----------------------------------------------
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54
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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55 ========= ===========================================
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56 Column Description
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57 --------- -------------------------------------------
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58 Type Record type
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59 Cluster Cluster number
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60 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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61 %Id Identity to the seed(as a percentage), or * if this is a seed.
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62 Strand '+' plus strand, '-' minus strand, or '.' amino acids.
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63 Qlo 0-based coordinate of alignment start in the query sequence.
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64 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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65 Alignment Compressed representation of alignment to the seed(see below), or '*' if a seed.
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66 Query FASTA label of query sequence
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67 Target FASTA label of target(seed / library / database) sequence. or '*' if a seed.
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68 ========= ===========================================
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69
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70 Record Types are:
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71 -----------------
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72
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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73 ====== ===========================================
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74 Column Description
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75 ------ -------------------------------------------
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76 L Library seed(generated only if a match if found to this seed).
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77 S New seed.
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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78 H Hit, also known as an accept; i.e. a successful match.
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79 D Library cluster.
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80 C New cluster.
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81 N Not matched (a sequence that didn't match library with --libonly specified).
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82 R Reject (generated only if --output_rejects is specified)
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 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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86 --------------------------------------------------------------------------------------------------------------------------
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 ==== ====== ============== =============
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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89 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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90 ---- ------ -------------- -------------
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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91 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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92 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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93 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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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 --------
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
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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99 </help>
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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100
e85e7ba38aff "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"
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101 </tool>