Mercurial > repos > iuc > concoct_merge_cut_up_clustering

comparison merge_cut_up_clustering.xml @ 2:21ccf9548e2c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
author iuc
date Thu, 07 Jul 2022 08:33:59 +0000
parents b546422c9128
children 20ccec4a2c38
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1:ce1a3ce0e807 2:21ccf9548e2c
1 <tool id="concoct_merge_cut_up_clustering" name="CONCOCT: merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="concoct_merge_cut_up_clustering" name="CONCOCT: Merge cut clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>into the original</description> 2 <description>and assign concensus clusters for the original contigs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/merge_cut_up_clustering.py' 8 merge_cutup_clustering.py
9 --input '$input' 9 '$cutup_clustering_result'
10 --output '$output' 10 > '$output'
11 ]]></command> 11 ]]></command>
12 <inputs> 12 <inputs>
13 <param name="input" type="data" format="tabular" label="Tabular file containng cut up contigs"/> 13 <param name="cutup_clustering_result" type="data" format="csv" label="Clusters generated by CONCOCT"/>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data name="output" format="tabular"/> 16 <data name="output" format="csv"/>
17 </outputs> 17 </outputs>
18 <tests> 18 <tests>
19 <!-- default settings --> 19 <!-- default settings -->
20 <test expect_num_outputs="1"> 20 <test expect_num_outputs="1">
21 <param name="input" value="input_merge_clusters.tabular" ftype="tabular"/> 21 <param name="cutup_clustering_result" value="clusters.csv" ftype="csv"/>
22 <output name="output" file="output_merge_clusters.tabular" ftype="tabular"/> 22 <output name="output" ftype="csv">
23 <assert_contents>
24 <has_size value="6923"/>
25 <has_text text="contig-21000001,39"/>
26 </assert_contents>
27 </output>
23 </test> 28 </test>
24 </tests> 29 </tests>
25 <help><![CDATA[ 30 <help><![CDATA[
26 **What it does** 31 **What it does**
27 32
28 Accepts a tbular file containing clusters output by the CONCOCT metagenome binning tool 33 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.
29 and produces a tabular file of the original contigs, with consecutive slices merged.
30 34
31 @HELP_OVERVIEW@ 35 @HELP_OVERVIEW@
32 ]]></help> 36 ]]></help>
33 <expand macro="citations"/> 37 <expand macro="citations"/>
34 </tool> 38 </tool>