Mercurial > repos > iuc > metabat2_jgi_summarize_bam_contig_depths

annotate jgi_summarize_bam_contig_depths.xml @ 0:d27a4ed006ee 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 12:21:33 +0000
parents
children 1592150e38d2
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d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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1 <tool id="metabat2_jgi_summarize_bam_contig_depths" name="Calculate contig depths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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2 <description>for MetaBAT2</description>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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3 <macros>
d27a4ed006ee "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>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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5 </macros>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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6 <expand macro="requirements"/>
d27a4ed006ee "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[
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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8 jgi_summarize_bam_contig_depths
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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9 --outputDepth '$outputDepth'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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10 --percentIdentity $advanced.percentIdentity
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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11 #if str($advanced.output_paired_contigs) == 'yes':
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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12 --pairedContigs '$outputPairedContigs'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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13 #end if
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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14 $advanced.noIntraDepthVariance
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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15 $advanced.showDepth
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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16 --minMapQual $advanced.minMapQual
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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17 --weightMapQual $advanced.weightMapQual
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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18 $advanced.includeEdgeBases
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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19 --maxEdgeBases $advanced.maxEdgeBases
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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20 #if str($advanced.use_reference_cond.use_reference) == 'yes':
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21 #if str($advanced.use_reference_cond.reference_cond.reference_source) == 'cached'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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22 --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta.fields.path'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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23 #else:
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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24 --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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25 #end if
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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26 --outputGC '$outputGC'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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27 --gcWindow $advanced.use_reference_cond.gcWindow
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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28 --outputReadStats '$outputReadStats'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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29 --outputKmers '$outputKmers'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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30 #end if
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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31 --shredLength $shredding.shredLength
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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32 --shredDepth $shredding.shredDepth
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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33 --minContigLength $shredding.minContigLength
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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34 --minContigDepth $shredding.minContigDepth
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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35 #for bam_input in $bam_inputs:
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36 '$bam_input'
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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37 #end for
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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38 ]]></command>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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39 <inputs>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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40 <param name="bam_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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41 <section name="advanced" title="Advanced options">
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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42 <param argument="--percentIdentity" type="integer" value="97" label="Minimum end-to-end percent identity of qualifying reads"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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43 <param name="output_paired_contigs" type="select" display="radio" label="Output the sparse matrix of contigs which paired reads span?">
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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44 <option value="no" selected="true">No</option>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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45 <option value="yes">Yes</option>
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46 </param>
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47 <param argument="--noIntraDepthVariance" type="boolean" truevalue="--noIntraDepthVariance" falsevalue="" checked="false" label="Remove variance from mean depth along the contig?"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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48 <param argument="--showDepth" type="boolean" truevalue="--showDepth" falsevalue="" checked="false" label="Output a depth file per bam for each contig base?"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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49 <param argument="--minMapQual" type="integer" value="0" label="Minimum mapping quality necessary to count a read as mapped"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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50 <param argument="--weightMapQual" type="float" value="0.0" label="Weight per-base depth based on the MQ of the read" help="Zero value disables"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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51 <param argument="--includeEdgeBases" type="boolean" truevalue="--includeEdgeBases" falsevalue="" checked="false" label="Include 1-readlength edges when calculating depth and variance?"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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52 <param argument="--maxEdgeBases" type="integer" value="75" label="Maximum length when calculating depth and variance" help="Ignored when including 1-readlength edges when calculating depth and variance"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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53 <conditional name="use_reference_cond">
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54 <param name="use_reference" type="select" label="Select a reference genome?">
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55 <option value="no" selected="true">No</option>
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56 <option value="yes">Yes</option>
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57 </param>
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58 <when value="no"/>
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59 <when value="yes">
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60 <conditional name="reference_cond">
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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61 <param name="reference_source" type="select" label="Choose the source for the reference genome">
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62 <option value="cached" selected="true">locally cached</option>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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63 <option value="history">from history</option>
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64 </param>
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65 <when value="cached">
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66 <param argument="--referenceFasta" type="select" label="Using reference genome">
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67 <options from_data_table="fasta_indexes">
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68 <filter type="data_meta" column="1" key="dbkey" ref="bam_inputs"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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69 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
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70 </options>
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71 </param>
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72 </when>
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73 <when value="history">
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74 <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/>
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75 </when>
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76 </conditional>
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77 <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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78 </when>
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79 </conditional>
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80 </section>
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81 <section name="shredding" title="Options to control shredding contigs that are under-represented by the reads">
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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82 <param argument="--shredLength" type="integer" value="16000" label="Maximum length of the shreds"/>
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83 <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/>
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84 <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/>
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85 <param argument="--minContigDepth" type="float" value="0.0" label="Minimum depth along the contig at which to break the contig"/>
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86 </section>
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87 </inputs>
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88 <outputs>
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89 <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string} (depth matrix)"/>
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90 <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string} (paired contigs)">
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91 <filter>advanced["output_paired_contigs"] == "yes"</filter>
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92 </data>
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93 <data name="outputGC" format="tabular" label="${tool.name} on ${on_string} (gc coverage histogram)">
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94 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter>
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95 </data>
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96 <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string} (read statistics)">
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97 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter>
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98 </data>
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99 <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string} (perfect kmer counts)">
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100 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <!-- Single input, default settings -->
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105 <test expect_num_outputs="1">
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106 <param name="bam_inputs" value="input1.bam" ftype="bam"/>
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107 <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/>
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108 </test>
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109 <!-- Multiple inputs, default settings -->
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110 <test expect_num_outputs="1">
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111 <param name="bam_inputs" value="input1.bam,input1.bam" ftype="bam"/>
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112 <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/>
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113 </test>
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114 <!-- Single input, output paired contigs, reference from history -->
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115 <test expect_num_outputs="5">
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116 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/>
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117 <param name="output_paired_contigs" value="yes"/>
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118 <param name="use_reference" value="yes"/>
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119 <param name="reference_source" value="history"/>
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120 <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/>
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121 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
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122 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
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123 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
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124 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
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125 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
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126 </test>
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127 <!-- Single input, output paired contigs, cached reference -->
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128 <test expect_num_outputs="5">
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129 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/>
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130 <param name="output_paired_contigs" value="yes"/>
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131 <param name="use_reference" value="yes"/>
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132 <param name="reference_source" value="cached"/>
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133 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
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134 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
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135 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
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136 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
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137 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
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138 </test>
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139 </tests>
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140 <help>
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141 **What it does**
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142
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143 Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)
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144 having mean and variance of base coverage depth that can be used as one of the inputs for the MetaBAT2 metagenome binning
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145 tool.
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146
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147 The algorithm used for calculating the coverage depth is adjusted by a few factors to improve the fidelity of the metrics
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148 when correlating abundance coverage in the binning stage. By default the following adjustments are applied.
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149
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150 **Edge bases are ignored**
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151
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152 Edge bases are not counted as coverage, by the lesser of 1 AverageReadLength or (--maxEdgeBases=75). This is because most
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153 mappers can not reliably place a read that would extend off the edge of a sequence, and coverage depth tends to drop towards
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154 0 at the edge of a contig or scaffold. Use --includeEdgeBases to include the coverage in this region.
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155
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156 **Reads with high mapping errors are skipped**
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157
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158 Reads that map imperfectly are excluded when the %ID of the mapping drops below a threshold (--percentIdentity=97).
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159 MetaBAT2 is designed to resolve strain variation and mapping reads with low %ID indicate that the read actually came from
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160 a different strain/species.
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161
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162 %ID is calculated from the CIGAR string and/or NM/MD fields and == 100 * MatchedBases / (MatchedBases + Substituions +
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163 Insertions + Deletions). This ensures that clips, insertions, deletions and mismatches are excluded from the coverage count.
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164 Only the read bases that exactly match the reference are counted as coverage. This generally has a small effect, except in
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165 the case of long reads from PacBio and Nanopore.
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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166
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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167 **More information**
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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168
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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169 https://bitbucket.org/berkeleylab/metabat/src/master/
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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170
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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171 **Options**
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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172
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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173 * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts.
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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174
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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175 </help>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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176 <expand macro="citations"/>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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177 </tool>
d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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178