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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author | iuc |
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date | Fri, 16 Aug 2024 08:59:54 +0000 |
parents | 78ff575ef835 |
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<tool id="ampvis2_merge_ampvis2" name="ampvis2 merge ampvis2 data sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="header"/> <command detect_errors="exit_code"><![CDATA[ Rscript '$rscript' ]]></command> <configfiles> <configfile name="rscript"><![CDATA[ library(ampvis2, quietly = TRUE) merged <- amp_merge_ampvis2( #for d in $data readRDS("$d"), #end for by_refseq = $by_refseq ) saveRDS(merged, "$output") merged ]]></configfile> </configfiles> <inputs> <expand macro="rds_input_macro" multiple="true"/> <param argument="by_refseq" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Merge by exact matches between DNA reference sequences" help="The full DNA sequences will then be used as the new names in the output."/> <!-- TODO refseq_names = NULL, rename_unmatched = TRUE, unmatched_prefix = "unmatched" --> </inputs> <outputs> <data name="output" format="ampvis2"/> </outputs> <tests> <!-- defaults --> <test expect_num_outputs="1"> <param name="data" value="AalborgWWTPs.2010.rds,AalborgWWTPs.2011.rds" ftype="ampvis2"/> <output name="output" ftype="ampvis2"> <assert_contents> <has_size value="70888" delta="1000"/> </assert_contents> </output> <assert_stdout> <!--check that the merged data has 13 samples--> <has_text text="13 125 6714 193 1019 475"/> </assert_stdout> </test> </tests> <help><![CDATA[ What it does ============ Merge any number of ampvis2 data sets into a single data set. The Galaxy tool calls the `amp_merge_ampvis2 <https://kasperskytte.github.io/ampvis2/reference/amp_merge_ampvis2.html>`_ function of the ampvis2 package. Input ===== @HELP_RDS_INPUT@ Details ======= It's important to ensure that the taxonomy for all OTU's across data sets is generated in the exact same way with the same database. When **Merge by exact matches between DNA reference sequences** is not checked it's likewise important to ensure that OTU ID's are not arbitrary between data sets and that they are corresponding to the same sequences across data sets (objects). When **Merge by exact matches between DNA reference sequences** is checked the full DNA sequences will be used as the new OTU ID's. Currently, phylogenetic trees are not merged. Output ====== The merged data set ]]></help> <expand macro="citations"/> </tool>