Mercurial > repos > iuc > ampvis2_octave

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9fe04d29ea604a152144908dbd20c0754695a025
author iuc
date Sat, 16 Nov 2024 19:56:46 +0000
parents 4289db874e3c
children
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b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_octave" name="ampvis2 octave plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(ampvis2, quietly = TRUE)
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13 d <- readRDS("$data")
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14 plot <- amp_octave(
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15 d,
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16 tax_aggregate = "$tax_aggregate",
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17 #if $group_by
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18 group_by = "$group_by",
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19 #if $scales
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20 scales = "$scales",
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21 #end if
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22 #end if
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23 num_threads = 1
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24 )
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25 @OUTPUT_TOKEN@
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26 ]]></configfile>
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27 </configfiles>
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28 <inputs>
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29 <expand macro="rds_metadata_input_macro"/>
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30 <expand macro="taxlevel_macro" argument="tax_aggregate" label="Aggregate (sum) OTU's to a taxonomic level initially." help="OTU's that have not been assigned at the chosen level will be removed with a message.">
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31 <option value="OTU" selected="true">OTU/ASV</option>
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32 </expand>
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33 <expand macro="metadata_select" argument="group_by" label="Group the samples based on a metadata variable." help="Variable needs to be categorical/discrete"/>
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34 <expand macro="facet_scales_macro" argument="scales" help="Only relevant if for group_by a value is selected"/>
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35 <expand macro="out_format_macro"/>
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36 </inputs>
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37 <outputs>
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38 <expand macro="out_macro"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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43 <output name="plot" value="AalborgWWTPs-octave.pdf" ftype="pdf" compare="sim_size"/>
0
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44 </test>
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45 <test>
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46 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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47 <param name="tax_aggregate" value="Class"/>
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48 <param name="out_format" value="png"/>
3
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49 <output name="plot" value="AalborgWWTPs-octave.png" ftype="png" compare="sim_size"/>
0
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50 </test>
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51 <test>
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52 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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53 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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54 <param name="group_by" value="Year"/>
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55 <param name="scales" value="free"/>
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56 <param name="out_format" value="svg"/>
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57 <output name="plot" value="AalborgWWTPs-octave.svg" ftype="svg" compare="sim_size"/>
0
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 What it does
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62 ============
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63
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64 Generates an octave plot to assess alpha diversity. An octave plot is a
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65 histogram of the number of taxa observed by bins of read counts, where the bin
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66 ranges increase exponentially, see details.
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67
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68 The Galaxy tool calls the `amp_octave
2
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69 <https://kasperskytte.github.io/ampvis2/reference/amp_octave.html>`_ function
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70 of the ampvis2 package.
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71
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72
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73 Details
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74 =======
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75
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76 The n-th bin in the histogram has the range ``r(n)=2n...2n+1-1``. The height of the
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77 bars then reflect the number of unique taxa with read counts in each bin. By
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78 judging the distribution one can assess whether the samples have been sequenced
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79 deeply enough at the chosen taxonomic level. A full symmetrical bell-shaped
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80 distribution with the left part far from the y-axis is the ideal. A high amount
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81 of OTU's with a low amount of reads indicates noise, chimeras, and even cross
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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82 talk.
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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83
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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84 Aggregating OTU's using ``tax_aggregate`` is useful to assess whether the samples
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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85 have been sequenced deep enough to capture the full diversity at the given
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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86 level, but ONLY applies to OTU's that have assigned taxonomy at the given level.
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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87
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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88 It is recommended to look at samples individually as grouping samples will
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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89 almost always look ideal. It is better to identify "bad" samples individually
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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90 and remove them.
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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91
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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92 Input
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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93 =====
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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94
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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95 @HELP_RDS_INPUT@
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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96
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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97 @HELP_METADATA_LIST_INPUT@
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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98
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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99 Output
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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100 ======
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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101
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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102 Octave plot in the chosen output format.
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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103
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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104 ]]></help>
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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105 <expand macro="citations"/>
b7f7d0c6d579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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106 </tool>