Mercurial > repos > iuc > concoct_merge_cut_up_clustering
diff merge_cut_up_clustering.xml @ 2:21ccf9548e2c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
author | iuc |
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date | Thu, 07 Jul 2022 08:33:59 +0000 |
parents | b546422c9128 |
children | 20ccec4a2c38 |
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--- a/merge_cut_up_clustering.xml Fri Jul 01 14:16:08 2022 +0000 +++ b/merge_cut_up_clustering.xml Thu Jul 07 08:33:59 2022 +0000 @@ -1,32 +1,36 @@ -<tool id="concoct_merge_cut_up_clustering" name="CONCOCT: merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>into the original</description> +<tool id="concoct_merge_cut_up_clustering" name="CONCOCT: Merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>and assign concensus clusters for the original contigs</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -python '$__tool_directory__/merge_cut_up_clustering.py' ---input '$input' ---output '$output' +merge_cutup_clustering.py + '$cutup_clustering_result' + > '$output' ]]></command> <inputs> - <param name="input" type="data" format="tabular" label="Tabular file containng cut up contigs"/> + <param name="cutup_clustering_result" type="data" format="csv" label="Clusters generated by CONCOCT"/> </inputs> <outputs> - <data name="output" format="tabular"/> + <data name="output" format="csv"/> </outputs> <tests> <!-- default settings --> <test expect_num_outputs="1"> - <param name="input" value="input_merge_clusters.tabular" ftype="tabular"/> - <output name="output" file="output_merge_clusters.tabular" ftype="tabular"/> + <param name="cutup_clustering_result" value="clusters.csv" ftype="csv"/> + <output name="output" ftype="csv"> + <assert_contents> + <has_size value="6923"/> + <has_text text="contig-21000001,39"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ **What it does** -Accepts a tbular file containing clusters output by the CONCOCT metagenome binning tool -and produces a tabular file of the original contigs, with consecutive slices merged. +This tool merges the clustering created by concoct by looking at cluster assignments per contig part and assigning a concensus cluster for the original contig. The output contains a header line and contig_id and cluster_id per line, separated by a comma. @HELP_OVERVIEW@ ]]></help>