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comparison binning_refiner.xml @ 0:f350d182f786 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
author iuc
date Fri, 18 Feb 2022 13:12:43 +0000
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1 <tool id="bin_refiner" name="Binning refiner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>refines metagenome bins</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9
10 ## Binning refiner prepends the -p param value
11 ## (which we set to be the string 'refined' in
12 ## the command line) to a hard-coded string (i.e.,
13 ## '_Binning_refiner_outputs') to set the base
14 ## output directory.
15
16 ## Binning_refiner requires 2 levels of directories
17 ## for the input bins.
18 mkdir -p input_bin_dir/bins &&
19 #for $f in $input_bins:
20 #set identifier = re.sub('[^\s\w\-]', '_', str($f.element_identifier))
21 #set file_name = $identifier + '.' + $f.ext
22 ## Binning_refiner doesn't handle gzipped files.
23 #if $f.ext.endswith(".gz")
24 gunzip -c '${f}' > 'input_bin_dir/bins/${file_name}' &&
25 #else:
26 ln -s '${f}' 'input_bin_dir/bins/${file_name}' &&
27 #end if
28 #end for
29
30 Binning_refiner
31 -i input_bin_dir
32 -p 'refined'
33 && mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs'
34 && mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length'
35 ]]></command>
36 <inputs>
37 <param name="input_bins" format="fasta,fasta.gz" type="data" multiple="true" label="Binned fasta files"/>
38 <param argument="-m" type="integer" value="512" label="Minimum size (Kbp) of refined bin" help="Bins smaller than this will be eliminated"/>
39 </inputs>
40 <outputs>
41 <collection name="output_refined_bins" type="list" label="${tool.name} on ${on_string}: (refined bins)">
42 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fasta" format="fasta" directory="refined_Binning_refiner_outputs/refined_refined_bins"/>
43 </collection>
44 <data name="output_refined_contigs" format="tabular" label="${tool.name} on ${on_string} (refined contigs)"/>
45 <data name="output_sources_and_length" format="tabular" label="${tool.name} on ${on_string} (sources and length)"/>
46 </outputs>
47 <tests>
48 <test expect_num_outputs="3">
49 <param name="input_bins" value="MetaBAT_17.fa.gz,MetaBAT_18.fa.gz,MetaBAT_19.fa.gz,MetaBAT_20.fa.gz,MetaBAT_21.fa.gz,MetaBAT_22.fa.gz,MetaBAT_23.fa.gz,Concoct_1.fa.gz,Concoct_3.fa.gz,Concoct_8.fa.gz" ftype="fasta.gz"/>
50 <output_collection name="output_refined_bins" type="list" count="7">
51 <element name="refined_1" ftype="fasta">
52 <assert_contents>
53 <has_size value="1320640"/>
54 <has_text text=">scaffold_2064"/>
55 <has_n_lines n="21765"/>
56 </assert_contents>
57 </element>
58 <element name="refined_2" ftype="fasta">
59 <assert_contents>
60 <has_size value="941488"/>
61 <has_text text=">scaffold_1301"/>
62 <has_n_lines n="15461"/>
63 </assert_contents>
64 </element>
65 <element name="refined_3" ftype="fasta">
66 <assert_contents>
67 <has_size value="883642"/>
68 <has_text text=">scaffold_262"/>
69 <has_n_lines n="14495"/>
70 </assert_contents>
71 </element>
72 <element name="refined_4" ftype="fasta">
73 <assert_contents>
74 <has_size value="758509"/>
75 <has_text text=">scaffold_923"/>
76 <has_n_lines n="12484"/>
77 </assert_contents>
78 </element>
79 <element name="refined_5" ftype="fasta">
80 <assert_contents>
81 <has_size value="722197"/>
82 <has_text text=">scaffold_232"/>
83 <has_n_lines n="11849"/>
84 </assert_contents>
85 </element>
86 <element name="refined_6" ftype="fasta">
87 <assert_contents>
88 <has_size value="637342"/>
89 <has_text text=">scaffold_259"/>
90 <has_n_lines n="10460"/>
91 </assert_contents>
92 </element>
93 <element name="refined_7" ftype="fasta">
94 <assert_contents>
95 <has_size value="560996"/>
96 <has_text text=">scaffold_1510"/>
97 <has_n_lines n="9219"/>
98 </assert_contents>
99 </element>
100 </output_collection>
101 <output name="output_refined_contigs" file="output_refined_contigs.tabular" ftype="tabular"/>
102 <output name="output_sources_and_length" file="output_sources_and_length.tabular" ftype="tabular"/>
103 </test>
104 </tests>
105 <help><![CDATA[
106 **What it does**
107
108 Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,
109 especially with respect to contamination levels.
110
111 The tool accepts one or more fasta datasets (i.e., bins) that were produced by metagenome binning tools
112 (CONCOCT MaxBin2, MetaBAT2 and others).
113
114 All refined bins larger than the specified "Minimum size (Kbp) of refined bin" will be output as a dataset
115 collection of fasta files. Additional outputs include a tabular dataset containing the id of the contigs
116 in each refined bin (refined contigs) and another tabular dataset containing the size of each refined bin
117 and the origin of its contigs (sources and length).
118
119 **More information**
120
121 https://github.com/songweizhi/Binning_refiner
122
123 ]]></help>
124 <expand macro="citations"/>
125 </tool>