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comparison metabat2.xml @ 0:76bc4efa1aeb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
author iuc
date Fri, 28 Jan 2022 12:21:05 +0000
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children 708abf08a626
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-1:000000000000 0:76bc4efa1aeb
1 <tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>metagenome binning</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir bins &&
9 metabat2
10 --inFile '$inFile'
11 --outFile 'bins/bin'
12 #if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes':
13 #if $advanced.base_coverage_depth_cond.abdFile:
14 --abdFile '$advanced.base_coverage_depth_cond.abdFile'
15 #else if $advanced.base_coverage_depth_cond.cvExt:
16 --cvExt '$advanced.base_coverage_depth_cond.cvExt'
17 #end if
18 #end if
19 --minContig $advanced.minContig
20 --maxP $advanced.maxP
21 --minS $advanced.minS
22 --maxEdges $advanced.maxEdges
23 --pTNF $advanced.pTNF
24 $advanced.noAdd
25 --minCV $advanced.minCV
26 --minCVSum $advanced.minCVSum
27 --minClsSize $advanced.minClsSize
28 --numThreads \${GALAXY_SLOTS:-4}
29 $advanced.onlyLabel
30 #if $advanced.saveCls:
31 $advanced.saveCls
32 --noBinOut
33 #end if
34 $advanced.unbinned
35 --seed $advanced.seed
36 > process_log.txt
37 #if str($advanced.output_process_log) == 'yes':
38 && mv process_log.txt '$process_log'
39 #end if
40 ]]></command>
41 <inputs>
42 <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
43 <section name="advanced" title="Advanced options">
44 <conditional name="base_coverage_depth_cond">
45 <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
46 <option value="no" selected="true">No</option>
47 <option value="yes">Yes</option>
48 </param>
49 <when value="no"/>
50 <when value="yes">
51 <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/>
52 <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/>
53 </when>
54 </conditional>
55 <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/>
56 <param argument="--maxP" type="integer" min="1" max="100" value="95" label="Percentage of good contigs considered for binning decided by connection among contigs" help="The greater, the more sensitive"/>
57 <param argument="--minS" type="integer" min="1" max="99" value="60" label="Minimum score of an edge for binning" help="The greater, the more specific"/>
58 <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
59 <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/>
60 <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
61 <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
62 <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/>
63 <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
64 <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
65 <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
66 <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/>
67 <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
68 <param name="output_process_log" type="select" label="Output process log file?">
69 <option value="no" selected="true">No</option>
70 <option value="yes">Yes</option>
71 </param>
72 </section>
73 </inputs>
74 <outputs>
75 <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)">
76 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="bins"/>
77 </collection>
78 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
79 <filter>advanced['output_process_log'] == 'yes'</filter>
80 </data>
81 </outputs>
82 <tests>
83 <test expect_num_outputs="1">
84 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
85 <param name="seed" value="345678"/>
86 <output_collection name="bin_files" type="list" count="2">
87 <element name="bin.1" ftype="fasta">
88 <assert_contents>
89 <has_size value="334554"/>
90 </assert_contents>
91 </element>
92 <element name="bin.2" ftype="fasta">
93 <assert_contents>
94 <has_size value="577866"/>
95 </assert_contents>
96 </element>
97 </output_collection>
98 </test>
99 <test expect_num_outputs="2">
100 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
101 <param name="base_coverage_depth" value="yes"/>
102 <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
103 <param name="seed" value="345678"/>
104 <param name="output_process_log" value="yes"/>
105 <output_collection name="bin_files" type="list" count="0"/>
106 <output name="process_log" file="process_log.txt" ftype="txt"/>
107 </test>
108 </tests>
109 <help><![CDATA[
110 **What it does**
111
112 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning
113 software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. The
114 tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files.
115
116 MetaBAT2 includes optionizations to MetaBAT. It requires virtually no parameter optimization. Default parameter
117 values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter.
118 Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing
119 the amount of data used for the analysis.
120
121 **More information**
122
123 https://bitbucket.org/berkeleylab/metabat/src/master/
124
125 **Options**
126
127 * **Use base coverage depth file** - optionally select a base coverage depth file that was either generated by the Calculate contig depths for MetaBAT2 tool or another 3rd party tool.
128
129 ]]></help>
130 <expand macro="citations"/>
131 </tool>