Mercurial > repos > iuc > ampvis2_octave

annotate octave.xml @ 4:84e959891258 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
author iuc
date Mon, 10 Nov 2025 12:54:44 +0000
parents a19a1fb784b7
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a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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6 <expand macro="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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11 <configfile name="rscript"><![CDATA[
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 d <- readRDS("$data")
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 plot <- amp_octave(
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 d,
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 tax_aggregate = "$tax_aggregate",
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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17 #if $group_by
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18 group_by = "$group_by",
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 #if $scales
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 scales = "$scales",
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 #end if
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22 #end if
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 num_threads = 1
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 )
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25 @OUTPUT_TOKEN@
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26 ]]></configfile>
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27 </configfiles>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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28 <inputs>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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29 <expand macro="rds_metadata_input_macro"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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.">
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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31 <option value="OTU" selected="true">OTU/ASV</option>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 </expand>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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34 <expand macro="facet_scales_macro" argument="scales" help="Only relevant if for group_by a value is selected"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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35 <expand macro="out_format_macro"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 </inputs>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <outputs>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <expand macro="out_macro"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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39 </outputs>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <tests>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 <test>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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42 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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43 <output name="plot" value="AalborgWWTPs-octave.pdf" ftype="pdf" compare="sim_size"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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44 </test>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <test>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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46 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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47 <param name="tax_aggregate" value="Class"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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48 <param name="out_format" value="png"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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49 <output name="plot" value="AalborgWWTPs-octave.png" ftype="png" compare="sim_size"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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50 </test>
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51 <test>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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52 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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53 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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54 <param name="group_by" value="Year"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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55 <param name="scales" value="free"/>
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56 <param name="out_format" value="svg"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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57 <output name="plot" value="AalborgWWTPs-octave.svg" ftype="svg" compare="sim_size"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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65 histogram of the number of taxa observed by bins of read counts, where the bin
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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77 bars then reflect the number of unique taxa with read counts in each bin. By
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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80 distribution with the left part far from the y-axis is the ideal. A high amount
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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81 of OTU's with a low amount of reads indicates noise, chimeras, and even cross
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82 talk.
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83
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84 Aggregating OTU's using ``tax_aggregate`` is useful to assess whether the samples
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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85 have been sequenced deep enough to capture the full diversity at the given
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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86 level, but ONLY applies to OTU's that have assigned taxonomy at the given level.
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87
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88 It is recommended to look at samples individually as grouping samples will
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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89 almost always look ideal. It is better to identify "bad" samples individually
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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90 and remove them.
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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91
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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92 Input
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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93 =====
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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94
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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95 @HELP_RDS_INPUT@
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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96
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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97 @HELP_METADATA_LIST_INPUT@
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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98
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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99 Output
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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100 ======
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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101
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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102 Octave plot in the chosen output format.
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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103
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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104 ]]></help>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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105 <expand macro="citations"/>
a19a1fb784b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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106 </tool>