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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 0f381ce2cdb0683f1bc8e1da321a5a75440bf619
author iuc
date Tue, 11 Mar 2025 12:23:05 +0000
parents 2a8bc1d26d06
children
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024ea3c4c29f planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/metawrapmg commit e8f404630d1b01ef5f110369f0cc6eac03d2d2d7
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1 <tool id="metawrapmg_binning" name="MetaWRAP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>metagenome binning pipeline</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## set memory usage
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10 if [ -n "\${GALAXY_MEMORY_MB}" ] ; then
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11 export GALAXY_MEMORY_GB="\$((GALAXY_MEMORY_MB / 1024))" ;
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12 fi ;
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14 ##################
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15 ## SET UP FILES ##
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16 ##################
0
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18 ## only plain FASTA and FASTQ
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19 ln -s '$metagenome' metagenome.fasta &&
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20 ## Metawrap checks for files named _1.fastq and _2.fastq.
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21 ln -s '$input.forward' reads_1.fastq &&
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22 ln -s '$input.reverse' reads_2.fastq &&
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23
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24 #####################
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25 ## INITIAL BINNING ##
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26 #####################
0
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27
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28 metawrap binning
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29 --metabat2 --maxbin2 --concoct
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30 -a metagenome.fasta
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31 -m "\${GALAXY_MEMORY_GB:-16}"
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32 -o INITIAL_BINNING
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33 -t "\${GALAXY_SLOTS:-4}"
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34 reads_1.fastq
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35 reads_2.fastq
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36 &&
0
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37
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38 ## Check which binning programs produced bins
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39 bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&
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40 switches=('-A' '-B' '-C') &&
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41
2
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42 i=0 &&
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43 bin_string="" &&
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44
2
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45 for dir in "\${bin_dirs[@]}" ; do
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46 if [ "\$(find "\$dir" -mindepth 1 -maxdepth 1 -exec echo found \;)" ]; then
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47 bin_string+=" \${switches[\$i]} \$dir" ;
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48 ((i++)) ;
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49 fi
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50 done &&
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51
2
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52 ####################
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53 ## BIN REFINEMENT ##
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54 ####################
0
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55
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56 ## The checkm database is in the conda package, see
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57 ## https://github.com/bioconda/bioconda-recipes/pull/38299.
0
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58
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59 metawrap bin_refinement
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60 -t "\${GALAXY_SLOTS:-4}"
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61 -m "\${GALAXY_MEMORY_GB:-16}"
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62 '$hidden_quick'
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63 -c '${binning.c}'
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64 -x '${binning.x}'
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65 -o BIN_REFINEMENT
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66 ## Only run bin_refinement on bins with contigs
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67 "\${bin_string}"
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68 ]]></command>
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69 <inputs>
2
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70 <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/>
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71 <param name="input" type="data_collection" collection_type="paired" label="Reads" help="Original reads that were used for the assembly"/>
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72 <section name="binning" title="Binning parameters" expanded="false">
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73 <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>
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74 <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>
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75 </section>
2
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76 <!-- the pplacer component requires 40 GB per thread. Skip pplacer for
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77 testing by setting this to "quick" -->
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78 <param name="hidden_quick" type="hidden" value=""/>
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79 </inputs>
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80 <outputs>
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81 <!-- contigs binned into fasta files -->
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82 <collection name="metawrap_bins" type="list" label="MetaWRAP on ${on_string}: bins">
2
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83 <discover_datasets pattern="metawrap_\d+_\d+_bins/(?P&lt;designation&gt;.+)\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true"/>
0
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84 </collection>
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85 <!-- summary figures -->
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86 <collection name="metawrap_figures" type="list" label="MetaWRAP on ${on_string}: summary figures">
2
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87 <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures"/>
0
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88 </collection>
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89 <!-- statistics on binning -->
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90 <collection name="metawrap_stats" type="list" label="MetaWRAP on ${on_string}: stat files">
2
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91 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.stats" format="tabular" directory="BIN_REFINEMENT"/>
0
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92 </collection>
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93 <!-- which contig went into which bin -->
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94 <collection name="metawrap_contigs" type="list" label="MetaWRAP on ${on_string}: contig assignments">
2
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95 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.contigs" format="tabular" directory="BIN_REFINEMENT"/>
0
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96 </collection>
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97 </outputs>
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98 <tests>
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99 <!-- 01: basic function -->
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100 <test>
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101 <param name="metagenome" value="subset.fasta.gz"/>
3
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102 <param name="input">
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103 <collection type="paired">
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104 <element name="forward" value="mapped_reads.r1.fastq.gz"/>
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105 <element name="reverse" value="mapped_reads.r2.fastq.gz"/>
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106 </collection>
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107 </param>
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108 <section name="binning">
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109 <param name="c" value="60"/>
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110 <param name="x" value="15"/>
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111 </section>
2
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112 <param name="hidden_quick" value="--quick"/>
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113 <output_collection name="metawrap_bins" type="list">
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114 <element name="bin.1" ftype="fasta">
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115 <assert_contents>
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116 <has_text text="NODE_2_length_"/>
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117 </assert_contents>
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118 </element>
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119 </output_collection>
0
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120 <output_collection name="metawrap_stats" type="list">
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121 <element name="metawrap_60_15_bins" file="test02.stats" ftype="tabular"/>
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122 </output_collection>
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123 <output_collection name="metawrap_contigs" type="list">
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124 <element name="metawrap_60_15_bins" file="test02.contigs" ftype="tabular"/>
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125 </output_collection>
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126 </test>
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127 </tests>
2
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128 <help><![CDATA[
0
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129 MetaWRAP
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130 --------
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131
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132 MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that
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133 accomplishes the core tasks of metagenomic analysis. Additionally,
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134 metaWRAP takes bin extraction and analysis to the next level. metaWRAP
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135 is meant to be a fast and simple approach before you delve deeper into
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136 parameterization of your analysis. MetaWRAP can be applied to a variety
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137 of environments, including gut, water, and soil microbiomes (see
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138 metaWRAP paper for benchmarks).
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139
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140 MetaWRAP binning module
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141 ~~~~~~~~~~~~~~~~~~~~~~~
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142
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143 The metaWRAP::Binning module is meant to be a convenient wrapper around
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144 three metagenomic binning software: MaxBin2, metaBAT2, and CONCOCT.
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145 First the metagenomic assembly is indexed with bwa-index, and then
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146 paired end reads from any number of samples are aligned to it. The
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147 alignments are sorted and compressed with samtools, and library insert
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148 size statistics are also gathered at the same time (insert size average
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149 and standard deviation). metaBAT2’s jgi_summarize_bam_contig_depths
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150 function is used to generate contig adundance table, and it is then
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151 converted into the correct format for each of the three binners to take
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152 as input. After MaxBin2, metaBAT2, and CONCOCT finish binning the
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153 contigs with default settings, the final bins folders are created with
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154 formatted bin fasta files. CheckM’s lineage_wf function is used to
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155 predict essential genes and estimate the completion and contamination of
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156 each bin.
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157
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158 MetaWRAP bin refinement
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159 ~~~~~~~~~~~~~~~~~~~~~~~
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160
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161 The metaWRAP::Bin_refinement module utilizes a hybrid approach to take
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162 in two or three bin sets that were obtained with different software and
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163 produces a consolidated, improved bin set. First, binning_refiner is
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164 used to create hybridized bins from every possible combination of sets.
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165 If there were three bin sets: A, B, and C, then the following hybrid
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166 sets will be produced with binning_refiner: AB, BC, AC, and ABC. CheckM
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167 is then run to evaluate the completion and contamination of the bins in
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168 each of the 7 bin sets (3 originals, 4 hybridized). The bins sets are
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169 then iteratively compared to each other, and each pair is consolidated
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170 into an improved bin set. To do this, the same bin is identified within
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171 the two bin sets based on a minimum of 80% overlap in genome length, and
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172 the better bin is determined based on which bin has the higher score.
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173 The scoring function is S=Completion-5*Contamination. After all bin sets
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174 are incorporated into the consolidated bin collection, a de-replication
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175 function removes any duplicate contigs. If a contig is present in more
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176 than one bin, it is removed from all but the best bin (based on scoring
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177 function). CheckM is then run on the final bin set and a final report
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178 file is generated showing the completion, contamination, and other
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179 statistics generated by CheckM for each bin. Completion and
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180 contamination rank plots are also generated to evaluate the success of
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181 the Bin_refinement module, and compare its output to the quality of the
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182 original bins.
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183
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184 --------------
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185
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186 MetaWRAP’s home page is
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187 `bxlab/metaWRAP <https://github.com/bxlab/metaWRAP>`__.
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188
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189 This tool was wrapped by the Galaxy Australia team.
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190 ]]></help>
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191 <expand macro="citations"/>
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192 </tool>