Mercurial > repos > iuc > concoct_extract_fasta_bins

comparison extract_fasta_bins.xml @ 0:1bc8fd1b3ed0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
author iuc
date Fri, 18 Feb 2022 14:17:48 +0000
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-1:000000000000 0:1bc8fd1b3ed0
1 <tool id="concoct_extract_fasta_bins" name="Extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for each cluster in a CONCOCT clustering file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir outdir &&
9 python '$__tool_directory__/extract_fasta_bins.py'
10 #if $input_fasta.is_of_type('fasta.gz'):
11 --gzipped
12 #end if
13 --input_fasta '$input_fasta'
14 --input_cluster '$input_cluster'
15 --output_path 'outdir'
16 ]]></command>
17 <inputs>
18 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="Fasta file"/>
19 <param argument="--input_cluster" type="data" format="tabular" label="CONCOCT clustering file"/>
20 </inputs>
21 <outputs>
22 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
23 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/>
24 </collection>
25 </outputs>
26 <tests>
27 <test expect_num_outputs="1">
28 <param name="input_fasta" value="input1.fa.gz" ftype="fasta.gz"/>
29 <param name="input_cluster" value="inputcluster1.tabular" ftype="tabular"/>
30 <output_collection name="bins" type="list" count="2">
31 <element name="77" ftype="fasta">
32 <assert_contents>
33 <has_size value="2194"/>
34 <has_text text="NODE_1_length_2054_cov_17.474684"/>
35 <has_n_lines n="37"/>
36 </assert_contents>
37 </element>
38 <element name="93" ftype="fasta">
39 <assert_contents>
40 <has_size value="16531"/>
41 <has_text text="NODE_2_length_16156_cov_8.219856"/>
42 <has_n_lines n="272"/>
43 </assert_contents>
44 </element>
45 </output_collection>
46 </test>
47 </tests>
48 <help><![CDATA[
49 **What it does**
50
51 Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a
52 CONCOCT clustering file.
53
54 The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using
55 the same fasta contigs input. A collection of fasta files is produced.
56 ]]></help>
57 <expand macro="citations"/>
58 </tool>