Mercurial > repos > iuc > ampvis2_frequency

annotate frequency.xml @ 7:467da4453127 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit d92935972ac18906154fadf42bd0c008e3c437e2
author iuc
date Fri, 25 Oct 2024 14:13:23 +0000
parents ac9564dcdb99
children
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f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_frequency" name="ampvis2 frequency plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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2 <description></description>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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6 <expand macro="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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8 Rscript '$rscript'
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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9 ]]></command>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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10 <configfiles>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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11 <configfile name="rscript"><![CDATA[
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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12 library(ampvis2, quietly = TRUE)
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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13 data <- readRDS("$data")
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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14 plot <- amp_frequency(
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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15 data,
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16 ## https://github.com/KasperSkytte/ampvis2/issues/167
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17 ## #if $group_by
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18 ## group_by = "$group_by",
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19 ## #end if
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20 ## tax_class = NULL,
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21 tax_empty = "$tax_empty",
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22 tax_aggregate = "$tax_aggregate",
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23 weight = $weight,
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24 normalise = $normalise,
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25 ## TODO
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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26 detailed_output = FALSE
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27 )
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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28 @OUTPUT_TOKEN@
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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29 ]]></configfile>
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30 </configfiles>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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31 <inputs>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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32 <expand macro="rds_metadata_input_macro"/>
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33 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
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34 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> -->
0
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35 <expand macro="tax_empty_macro"/>
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36 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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37 <option value="OTU" selected="true">OTU/ASV</option>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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38 </expand>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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39 <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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40 <expand macro="normalise_macro" checked="true"/>
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41 <expand macro="out_format_macro"/>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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42 </inputs>
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43 <outputs>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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44 <expand macro="out_macro"/>
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45 </outputs>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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46 <tests>
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47 <!-- defaults -->
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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48 <test expect_num_outputs="1">
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49 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
4
ac9564dcdb99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit ab75ba7665d7fb5c18ad08dfbba92b273f991dfc
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50 <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf" compare="sim_size"/>
0
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51 </test>
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52 <!-- group_by -->
3
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53 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
0
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54 <test expect_num_outputs="1">
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55 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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56 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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57 <param name="group_by" value="Plant"/>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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58 <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/>
3
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59 </test> -->
0
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60 </tests>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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61 <help><![CDATA[
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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62 What it does
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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63 ============
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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64
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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65 Generates a barplot with frequency vs read abundance.
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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66
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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67 The Galaxy tool calls the `amp_frequency
2
b8ecbc50af78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
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68 <https://kasperskytte.github.io/ampvis2/reference/amp_frequency.html>`_ function
0
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69 of the ampvis2 package.
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70
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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71 Input
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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72 =====
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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73
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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74 @HELP_RDS_INPUT@
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75
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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76 @HELP_METADATA_LIST_INPUT@
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77
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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78 Output
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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79 ======
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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80
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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81 A frequency plot in the chosen output format.
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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82 ]]></help>
f77f7c426d6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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83 <expand macro="citations"/>
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84 </tool>