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comparison export_fasta.xml @ 0:073d32dd1e02 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:50:38 +0000
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1 <tool id="ampvis2_export_fasta" name="ampvis2 export fasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="header"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE)
13 data <- readRDS("$data")
14 amp_export_fasta(data, filename = "$output", tax = $tax)
15 ]]></configfile>
16 </configfiles>
17 <inputs>
18 <expand macro="rds_input_macro"/>
19 <param argument="tax" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Add taxonomic strings to the output"/>
20 </inputs>
21 <outputs>
22 <data name="output" format="fasta"/>
23 </outputs>
24 <tests>
25 <!-- defaults -->
26 <test expect_num_outputs="1">
27 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
28 <output name="output" value="AalborgWWTPs.fa" ftype="fasta"/>
29 </test>
30 <!-- tax -->
31 <test expect_num_outputs="1">
32 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
33 <param name="tax" value="true"/>
34 <output name="output" ftype="fasta">
35 <assert_contents>
36 <has_text text=">OTU_2397; k__Bacteria; p__Chloroflexi; c__Anaerolineae; o__Anaerolineales; f__Anaerolineaceae; g__uncultured; s__"/>
37 <has_size value="125478"/>
38 </assert_contents>
39 </output>
40 </test>
41 </tests>
42 <help><![CDATA[
43 What it does
44 ============
45
46 Export sequences from an ampvis2 object and optionally add taxonomy to the fasta header lines.
47
48 The Galaxy tool calls the `amp_export_fasta
49 <https://kasperskytte.github.io/ampvis2/reference/amp_export_fasta.html>`_ function
50 of the ampvis2 package.
51
52 Input
53 =====
54
55 @HELP_RDS_INPUT@
56
57 In order to work the ampvis2 rds data set needs to contain sequence information.
58
59 Output
60 ======
61
62 The sequences contained in the input as fasta.
63
64 ]]></help>
65 <expand macro="citations"/>
66 </tool>