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annotate metabat2.xml @ 2:708abf08a626 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
author iuc
date Tue, 02 Aug 2022 09:40:59 +0000
parents 76bc4efa1aeb
children eb50e7eca3dc
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76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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1 <tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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2 <description>metagenome binning</description>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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3 <macros>
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4 <import>macros.xml</import>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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5 </macros>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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6 <expand macro="requirements"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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7 <command detect_errors="exit_code"><![CDATA[
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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8 mkdir bins &&
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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9 metabat2
2
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10 --inFile '$inFile'
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11 --outFile 'bins/bin'
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
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12 #if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes'
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13 #if $advanced.base_coverage_depth_cond.abdFile
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
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14 --abdFile '$advanced.base_coverage_depth_cond.abdFile'
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15 #else if $advanced.base_coverage_depth_cond.cvExt
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16 --cvExt '$advanced.base_coverage_depth_cond.cvExt'
0
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17 #end if
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18 #end if
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19 --minContig $advanced.minContig
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20 --maxP $advanced.maxP
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21 --minS $advanced.minS
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22 --maxEdges $advanced.maxEdges
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23 --pTNF $advanced.pTNF
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24 $advanced.noAdd
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25 --minCV $advanced.minCV
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26 --minCVSum $advanced.minCVSum
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27 --seed $advanced.seed
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28 --minClsSize $out.minClsSize
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29 --numThreads \${GALAXY_SLOTS:-4}
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
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30 $out.onlyLabel
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31 #if $out.saveCls
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32 $out.saveCls
0
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33 --noBinOut
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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34 #end if
2
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35 #if 'unbinned' in $out.extra_outputs
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36 --unbinned
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37 #end if
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38 > process_log.txt
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
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39 #if 'log' in $out.extra_outputs
0
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40 && mv process_log.txt '$process_log'
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41 #end if
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42 ]]></command>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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43 <inputs>
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44 <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
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45 <section name="advanced" title="Advanced options">
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46 <conditional name="base_coverage_depth_cond">
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47 <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
2
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48 <option value="yes">Yes</option>
0
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49 <option value="no" selected="true">No</option>
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50 </param>
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51 <when value="no"/>
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52 <when value="yes">
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53 <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"/>
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54 <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"/>
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55 </when>
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56 </conditional>
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57 <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/>
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58 <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"/>
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59 <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"/>
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60 <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
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61 <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)"/>
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62 <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
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63 <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
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64 <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"/>
2
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65 <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
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66 </section>
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67 <section name="out" title="Output options">
0
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68 <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
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69 <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
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70 <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
2
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71 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
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72 <option value="lowDepth">Fasta file containing low depth bins (if no matrix format and label selected)</option>
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73 <option value="tooShort">Fasta file containing too short bins (if no matrix format and label selected)</option>
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74 <option value="unbinned">Fasta file containing unbinned contigs (if no matrix format and label selected)</option>
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75 <option value="log">Process log file</option>
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76 </param>
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77 </section>
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78 </inputs>
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79 <outputs>
2
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80 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
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81 <filter>not out['saveCls'] and not out['onlyLabel']</filter>
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82 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
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83 </collection>
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84 <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins">
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85 <filter>out['saveCls'] and not out['onlyLabel']</filter>
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86 </data>
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87 <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins">
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88 <filter>not out['saveCls'] and out['onlyLabel']</filter>
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89 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
0
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90 </collection>
2
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91 <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
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92 <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>
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93 </data>
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94 <data name="tooShort" format="fasta" from_work_dir="bins/bin.tooShort.fa" label="${tool.name} on ${on_string}: Too short bins">
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95 <filter>not out['saveCls'] and not out['onlyLabel'] and 'tooShort' in out['extra_outputs']</filter>
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96 </data>
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97 <data name="unbinned" format="fasta" from_work_dir="bins/bin.unbinned.fa" label="${tool.name} on ${on_string}: Unbinned sequences">
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98 <filter>not out['saveCls'] and not out['onlyLabel'] and 'unbinned' in out['extra_outputs']</filter>
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99 </data>
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100 <data name="process_log" format="txt" label="${tool.name} on ${on_string}: Process log">
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101 <filter>'log' in out['extra_outputs']</filter>
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102 </data>
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103 </outputs>
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104 <tests>
2
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105 <test expect_num_outputs="5">
0
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106 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
2
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107 <section name="advanced">
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108 <conditional name="base_coverage_depth_cond">
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109 <param name="base_coverage_depth" value="no"/>
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110 </conditional>
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111 <param name="seed" value="345678"/>
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112 </section>
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113 <section name="out">
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114 <param name="extra_outputs" value="lowDepth,tooShort,unbinned,log"/>
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115 </section>
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116 <output_collection name="bins" type="list" count="2">
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117 <element name="1" ftype="fasta">
0
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118 <assert_contents>
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119 <has_size value="334554"/>
2
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120 <has_text text=">MW127517.1"/>
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121 <has_text text=">MW127521.1"/>
0
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122 </assert_contents>
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123 </element>
2
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124 <element name="2" ftype="fasta">
0
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125 <assert_contents>
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126 <has_size value="577866"/>
2
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127 <has_text text=">MT810119.1"/>
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128 <has_text text=">MW130866.1"/>
0
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129 </assert_contents>
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130 </element>
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131 </output_collection>
2
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132 <output name="lowDepth" ftype="fasta">
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133 <assert_contents>
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134 <has_text text=""/>
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135 </assert_contents>
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136 </output>
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137 <output name="tooShort" ftype="fasta">
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138 <assert_contents>
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139 <has_text text=""/>
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140 </assert_contents>
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141 </output>
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142 <output name="unbinned" ftype="fasta">
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143 <assert_contents>
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144 <has_text text=">NC_045512.2"/>
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145 <has_text text=">MW130872.1"/>
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146 </assert_contents>
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147 </output>
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148 <output name="process_log" ftype="txt">
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149 <assert_contents>
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150 <has_text text="MetaBAT"/>
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151 <has_text text="2 bins (897090 bases in total) formed"/>
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152 </assert_contents>
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153 </output>
0
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154 </test>
2
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155 <test expect_num_outputs="1">
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156 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
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157 <section name="advanced">
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158 <conditional name="base_coverage_depth_cond">
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159 <param name="base_coverage_depth" value="yes"/>
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160 <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
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161 </conditional>
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162 <param name="seed" value="345678"/>
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163 </section>
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164 <section name="out">
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165 <param name="onlyLabel" value="false"/>
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166 <param name="saveCls" value="false"/>
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167 <param name="extra_outputs" value=""/>
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168 </section>
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169 <output_collection name="bins" type="list" count="0"/>
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170 </test>
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171 <test expect_num_outputs="1">
0
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172 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
2
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173 <section name="advanced">
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174 <conditional name="base_coverage_depth_cond">
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175 <param name="base_coverage_depth" value="no"/>
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176 </conditional>
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177 <param name="seed" value="345678"/>
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178 </section>
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179 <section name="out">
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180 <param name="onlyLabel" value="false"/>
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181 <param name="saveCls" value="true"/>
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182 <param name="extra_outputs" value=""/>
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183 </section>
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184 <output name="bin_saveCls" ftype="tabular">
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185 <assert_contents>
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186 <has_text text="NC_045512.2"/>
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187 <has_text text="MT810119.1"/>
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188 <has_text text="MW130860.1"/>
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189 </assert_contents>
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190 </output>
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191 </test>
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192 <test expect_num_outputs="1">
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193 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
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194 <section name="advanced">
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195 <conditional name="base_coverage_depth_cond">
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196 <param name="base_coverage_depth" value="no"/>
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197 </conditional>
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198 <param name="seed" value="345678"/>
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199 </section>
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200 <section name="out">
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201 <param name="onlyLabel" value="true"/>
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202 <param name="saveCls" value="false"/>
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203 <param name="extra_outputs" value=""/>
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204 </section>
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205 <output_collection name="bin_onlyLabel" type="list" count="2">
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206 <element name="1" ftype="tabular">
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207 <assert_contents>
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208 <has_text text="MW127518.1"/>
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209 <has_text text="MW127521.1"/>
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210 </assert_contents>
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211 </element>
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212 <element name="2" ftype="tabular">
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213 <assert_contents>
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214 <has_text text="MT810119.1"/>
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215 <has_text text="MW130866.1"/>
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216 </assert_contents>
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217 </element>
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218 </output_collection>
0
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219 </test>
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220 </tests>
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221 <help><![CDATA[
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222 **What it does**
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223
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224 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning
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225 software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. The
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226 tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files.
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227
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228 MetaBAT2 includes optionizations to MetaBAT. It requires virtually no parameter optimization. Default parameter
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229 values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter.
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230 Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing
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231 the amount of data used for the analysis.
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232
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233 **More information**
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234
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235 https://bitbucket.org/berkeleylab/metabat/src/master/
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236
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237 **Options**
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238
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239 * **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.
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240
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241 ]]></help>
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242 <expand macro="citations"/>
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243 </tool>