Mercurial > repos > iuc > metabat2_jgi_summarize_bam_contig_depths
annotate jgi_summarize_bam_contig_depths.xml @ 0:d27a4ed006ee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
author | iuc |
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date | Fri, 28 Jan 2022 12:21:33 +0000 |
parents | |
children | 1592150e38d2 |
rev | line source |
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0
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"
iuc
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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"
iuc
parents:
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3 <macros> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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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"
iuc
parents:
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5 </macros> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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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"
iuc
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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"
iuc
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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"
iuc
parents:
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9 --outputDepth '$outputDepth' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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10 --percentIdentity $advanced.percentIdentity |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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11 #if str($advanced.output_paired_contigs) == 'yes': |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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12 --pairedContigs '$outputPairedContigs' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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13 #end if |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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14 $advanced.noIntraDepthVariance |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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15 $advanced.showDepth |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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18 $advanced.includeEdgeBases |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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19 --maxEdgeBases $advanced.maxEdgeBases |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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20 #if str($advanced.use_reference_cond.use_reference) == 'yes': |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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21 #if str($advanced.use_reference_cond.reference_cond.reference_source) == 'cached' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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22 --referenceFasta '$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"
iuc
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23 #else: |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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24 --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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25 #end if |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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26 --outputGC '$outputGC' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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27 --gcWindow $advanced.use_reference_cond.gcWindow |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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28 --outputReadStats '$outputReadStats' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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29 --outputKmers '$outputKmers' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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30 #end if |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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35 #for bam_input in $bam_inputs: |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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36 '$bam_input' |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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37 #end for |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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38 ]]></command> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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39 <inputs> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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45 <option value="yes">Yes</option> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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46 </param> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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53 <conditional name="use_reference_cond"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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54 <param name="use_reference" type="select" label="Select a reference genome?"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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55 <option value="no" selected="true">No</option> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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56 <option value="yes">Yes</option> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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57 </param> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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58 <when value="no"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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59 <when value="yes"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"
iuc
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61 <param name="reference_source" type="select" label="Choose the source for the reference genome"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"
iuc
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63 <option value="history">from history</option> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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64 </param> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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65 <when value="cached"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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66 <param argument="--referenceFasta" type="select" label="Using reference genome"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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67 <options from_data_table="fasta_indexes"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"
iuc
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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)"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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70 </options> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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71 </param> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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72 </when> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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73 <when value="history"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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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"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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75 </when> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
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76 </conditional> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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79 </conditional> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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80 </section> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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83 <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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84 <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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86 </section> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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87 </inputs> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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88 <outputs> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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89 <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string} (depth matrix)"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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90 <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string} (paired contigs)"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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91 <filter>advanced["output_paired_contigs"] == "yes"</filter> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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92 </data> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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93 <data name="outputGC" format="tabular" label="${tool.name} on ${on_string} (gc coverage histogram)"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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94 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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95 </data> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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96 <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string} (read statistics)"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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97 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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98 </data> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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99 <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string} (perfect kmer counts)"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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100 <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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101 </data> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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102 </outputs> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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103 <tests> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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104 <!-- Single input, default settings --> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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105 <test expect_num_outputs="1"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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106 <param name="bam_inputs" value="input1.bam" ftype="bam"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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107 <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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108 </test> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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109 <!-- Multiple inputs, default settings --> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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110 <test expect_num_outputs="1"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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111 <param name="bam_inputs" value="input1.bam,input1.bam" ftype="bam"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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112 <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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113 </test> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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114 <!-- Single input, output paired contigs, reference from history --> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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115 <test expect_num_outputs="5"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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116 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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117 <param name="output_paired_contigs" value="yes"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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118 <param name="use_reference" value="yes"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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119 <param name="reference_source" value="history"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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120 <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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121 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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122 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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123 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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124 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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125 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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126 </test> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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127 <!-- Single input, output paired contigs, cached reference --> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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128 <test expect_num_outputs="5"> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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129 <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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130 <param name="output_paired_contigs" value="yes"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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131 <param name="use_reference" value="yes"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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132 <param name="reference_source" value="cached"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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133 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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134 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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135 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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136 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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137 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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138 </test> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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139 </tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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140 <help> |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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141 **What it does** |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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142 |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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) |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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 |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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145 tool. |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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146 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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148 when correlating abundance coverage in the binning stage. By default the following adjustments are applied. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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149 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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150 **Edge bases are ignored** |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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151 |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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 |
d27a4ed006ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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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. |
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166 |
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167 **More information** |
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168 |
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169 https://bitbucket.org/berkeleylab/metabat/src/master/ |
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170 |
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171 **Options** |
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172 |
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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. |
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174 |
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175 </help> |
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176 <expand macro="citations"/> |
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177 </tool> |
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178 |