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