Mercurial > repos > iuc > ampvis2_frequency

comparison frequency.xml @ 3:cdba4eab5a54 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
author iuc
date Mon, 26 Feb 2024 07:54:14 +0000
parents b8ecbc50af78
children ac9564dcdb99
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2:b8ecbc50af78 3:cdba4eab5a54
11 <configfile name="rscript"><![CDATA[ 11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE) 12 library(ampvis2, quietly = TRUE)
13 data <- readRDS("$data") 13 data <- readRDS("$data")
14 plot <- amp_frequency( 14 plot <- amp_frequency(
15 data, 15 data,
16 #if $group_by 16 ## https://github.com/KasperSkytte/ampvis2/issues/167
17 group_by = "$group_by", 17 ## #if $group_by
18 #end if 18 ## group_by = "$group_by",
19 ## #end if
19 ## tax_class = NULL, 20 ## tax_class = NULL,
20 tax_empty = "$tax_empty", 21 tax_empty = "$tax_empty",
21 tax_aggregate = "$tax_aggregate", 22 tax_aggregate = "$tax_aggregate",
22 weight = $weight, 23 weight = $weight,
23 normalise = $normalise, 24 normalise = $normalise,
27 @OUTPUT_TOKEN@ 28 @OUTPUT_TOKEN@
28 ]]></configfile> 29 ]]></configfile>
29 </configfiles> 30 </configfiles>
30 <inputs> 31 <inputs>
31 <expand macro="rds_metadata_input_macro"/> 32 <expand macro="rds_metadata_input_macro"/>
32 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> 33 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
34 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> -->
33 <expand macro="tax_empty_macro"/> 35 <expand macro="tax_empty_macro"/>
34 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> 36 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
35 <option value="OTU" selected="true">OTU/ASV</option> 37 <option value="OTU" selected="true">OTU/ASV</option>
36 </expand> 38 </expand>
37 <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/> 39 <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/>
46 <test expect_num_outputs="1"> 48 <test expect_num_outputs="1">
47 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 49 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
48 <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf"/> 50 <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf"/>
49 </test> 51 </test>
50 <!-- group_by --> 52 <!-- group_by -->
53 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
51 <test expect_num_outputs="1"> 54 <test expect_num_outputs="1">
52 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 55 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
53 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 56 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
54 <param name="group_by" value="Plant"/> 57 <param name="group_by" value="Plant"/>
55 <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/> 58 <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/>
56 </test> 59 </test> -->
57 </tests> 60 </tests>
58 <help><![CDATA[ 61 <help><![CDATA[
59 What it does 62 What it does
60 ============ 63 ============
61 64