Mercurial > repos > iuc > concoct_extract_fasta_bins

comparison extract_fasta_bins.xml @ 3:bcd8d64f82b7 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 08:33:11 +0000
parents a04028a8181d
children 8b1b09fcd8b7
comparison
equal deleted inserted replaced
2:92a2d9109528 3:bcd8d64f82b7
1 <tool id="concoct_extract_fasta_bins" name="CONCOCT: extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="concoct_extract_fasta_bins" name="CONCOCT: Extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for each cluster</description> 2 <description>for each cluster</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 ## CONCOCT doesn't handle gzipped files.
9 #if $fasta_file.ext.endswith(".gz")
10 gunzip -c '$fasta_file' > 'contigs.fa' &&
11 #else:
12 ln -s '$fasta_file' 'contigs.fa' &&
13 #end if
14
8 mkdir outdir && 15 mkdir outdir &&
9 python '$__tool_directory__/extract_fasta_bins.py' 16 extract_fasta_bins.py
10 #if $input_fasta.is_of_type('fasta.gz'): 17 'contigs.fa'
11 --gzipped 18 '$cluster_file'
12 #end if 19 --output_path 'outdir'
13 --input_fasta '$input_fasta'
14 --input_cluster '$input_cluster'
15 --output_path 'outdir'
16 ]]></command> 20 ]]></command>
17 <inputs> 21 <inputs>
18 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="Fasta file"/> 22 <param name="fasta_file" type="data" format="fasta,fasta.gz" label="Original contig file"/>
19 <param argument="--input_cluster" type="data" format="tabular" label="CONCOCT clustering file"/> 23 <param name="cluster_file" type="data" format="csv" label="CONCOCT clusters"/>
20 </inputs> 24 </inputs>
21 <outputs> 25 <outputs>
22 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)"> 26 <collection name="bins" type="list" label="${tool.name} on ${on_string} : Bins">
23 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/> 27 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/>
24 </collection> 28 </collection>
25 </outputs> 29 </outputs>
26 <tests> 30 <tests>
27 <test expect_num_outputs="1"> 31 <test expect_num_outputs="1">
28 <param name="input_fasta" value="input1.fa.gz" ftype="fasta.gz"/> 32 <param name="fasta_file" value="composition.fa.gz" ftype="fasta.gz"/>
29 <param name="input_cluster" value="inputcluster1.tabular" ftype="tabular"/> 33 <param name="cluster_file" value="clusters.csv" ftype="csv"/>
30 <output_collection name="bins" type="list" count="2"> 34 <output_collection name="bins" type="list" count="54">
31 <element name="77" ftype="fasta"> 35 <element name="0" ftype="fasta">
32 <assert_contents> 36 <assert_contents>
33 <has_size value="2194"/> 37 <has_size value="1194"/>
34 <has_text text="NODE_1_length_2054_cov_17.474684"/> 38 <has_text text="contig-223000058 1140 nucleotides"/>
35 <has_n_lines n="37"/> 39 <has_n_lines n="20"/>
36 </assert_contents> 40 </assert_contents>
37 </element> 41 </element>
38 <element name="93" ftype="fasta"> 42 <element name="52" ftype="fasta">
39 <assert_contents> 43 <assert_contents>
40 <has_size value="16531"/> 44 <has_size value="5356"/>
41 <has_text text="NODE_2_length_16156_cov_8.219856"/> 45 <has_text text="contig-161000004 1031 nucleotides"/>
42 <has_n_lines n="272"/> 46 <has_n_lines n="90"/>
43 </assert_contents> 47 </assert_contents>
44 </element> 48 </element>
45 </output_collection> 49 </output_collection>
46 </test> 50 </test>
47 </tests> 51 </tests>
48 <help><![CDATA[ 52 <help><![CDATA[
49 **What it does** 53 **What it does**
50 54
51 Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a 55 Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a CONCOCT clustering file.
52 CONCOCT clustering file.
53 56
54 The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using 57 The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using the same fasta contigs input. A collection of fasta files is produced.
55 the same fasta contigs input. A collection of fasta files is produced.
56 58
57 @HELP_OVERVIEW@ 59 @HELP_OVERVIEW@
58 ]]></help> 60 ]]></help>
59 <expand macro="citations"/> 61 <expand macro="citations"/>
60 </tool> 62 </tool>