Mercurial > repos > iuc > ampvis2_rarecurve

annotate rarecurve.xml @ 8:094d0b97f92c draft default tip

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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 19:52:12 +0000
parents 2e69edaaa834
children
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65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_rarecurve" name="ampvis2 rarefaction curve" 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 '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(ampvis2, quietly = TRUE)
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13 data <- readRDS("$data")
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14 plot <- amp_rarecurve(
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15 data,
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16 stepsize = $stepsize
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17 #if $color_by
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18 , color_by = "$color_by",
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19 #end if
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20 #if $facet_by
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21 , facet_by = "$facet_by",
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22 #if $facet_scales
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23 , facet_scales = "$facet_scales"
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24 #end if
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25 #end if
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26 )
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27
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28 @OUTPUT_TOKEN@
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29 ]]></configfile>
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30 </configfiles>
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31 <inputs>
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32 <expand macro="rds_metadata_input_macro"/>
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33 <!-- TODO if no metadata_list is given that the color/facet_by selects
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34 give a warnings in the logs:
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35 WARNI [galaxy.tools.parameters.dynamic_options] could not create dynamic options from_dataset: metadata_list not a data or collection paramete
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36
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37 - introduce a conditional color_facet_cond wich optionally shows these options
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38 and make metadata_list required?
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39 - or use a filter + proper message instead of from_datatable ?
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40
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41 here and everywhere else -->
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42 <param argument="stepsize" type="integer" value="1000" min="1" label="Step size" help="Lower is prettier but takes more time to generate."/>
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43 <expand macro="metadata_select" argument="color_by" label="Color curves by"/>
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44 <expand macro="metadata_select_discrete" argument="facet_by" label="Facet curves by"/>
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45 <expand macro="facet_scales_macro" argument="facet_scales" help="Only relevant if for facet_by a value is selected"/>
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46 <expand macro="out_format_macro"/>
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47 </inputs>
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48 <outputs>
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49 <expand macro="out_macro"/>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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54 <output name="plot" value="AalborgWWTPs-rarecurve.pdf" ftype="pdf" compare="sim_size"/>
0
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55 </test>
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56 <test>
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57 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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58 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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59 <param name="stepsize" value="100"/>
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60 <param name="color_by" value="Plant"/>
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61 <output name="plot" value="AalborgWWTPs-rarecurve-color.pdf" ftype="pdf" compare="sim_size"/>
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62 </test>
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63 <test>
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64 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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65 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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66 <param name="stepsize" value="100"/>
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67 <param name="facet_by" value="Plant"/>
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68 <param name="facet_scales" value="fixed"/>
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69 <output name="plot" value="AalborgWWTPs-rarecurve-facet.pdf" ftype="pdf" compare="sim_size"/>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 What it does
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74 ============
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75
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76 Generates a rarefaction curve (number of reads vs number of observed OTUs) for each sample.
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77 The plot can be colored or faceted (i.e. split into multiple panels) by metadata
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78
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79 The Galaxy tool calls the `amp_rarecurve
2
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80 <https://kasperskytte.github.io/ampvis2/reference/amp_rarecurve.html>`_ function
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81 of the ampvis2 package.
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82
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83 Input
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84 =====
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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85
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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86 @HELP_RDS_INPUT@
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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87
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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88 @HELP_METADATA_LIST_INPUT@
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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89
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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90 Output
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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91 ======
65cc862ec3c4 "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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92
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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93 Rarefaction curves in the chosen output format.
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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94
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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95 ]]></help>
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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96 <expand macro="citations"/>
65cc862ec3c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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97 </tool>