Mercurial > repos > iuc > comebin

annotate comebin.xml @ 1:15f6ef1d7c96 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
author iuc
date Wed, 30 Jul 2025 11:47:15 +0000
parents 2576c9132481
children ddfb9c10740a
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2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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1 <tool id="comebin" name="COMEBin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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2 <description>Binning of metagenomic contigs using COntrastive Multi-viEw representation learning</description>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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3 <macros>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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4 <import>macros.xml</import>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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5 </macros>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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6 <expand macro="requirements"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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7 <command detect_errors="exit_code">
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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8 <![CDATA[
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9
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10 #import re
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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12 mkdir 'outputs' 'bam_files' &&
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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14 #set $safename = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier)
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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15 ln -s '$assembly_file' '${safename}.fasta' &&
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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17 #for $file in $bam_files:
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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18 #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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19 ln -s '$file' './bam_files/${safename}.bam' &&
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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20 #end for
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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22 run_comebin.sh
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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23 -a 'assembly_file.fasta'
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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24 -o 'outputs'
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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25 -p 'bam_files'
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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26 -t \${GALAXY_SLOTS:-12}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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27 -l ${loss}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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28 -n ${learning}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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29 -e ${emb_comebin}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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30 -c ${emb_cov}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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31 -b ${batch}
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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32
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33 ]]>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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34 </command>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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35 <inputs>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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36 <param name="assembly_file" type="data" format="fasta" label="Metagenomic assembly file"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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37 <param name="bam_files" type="data" format="bam" multiple="true" label="Input bam file(s)"/>
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15f6ef1d7c96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
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38 <param name="learning" type="integer" value="6" label="Views for contrastive multiple-view learning"/>
15f6ef1d7c96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
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39 <param name="loss" type="float" value="0.15" label="Temperature in loss function" help="0.07 is recommended for assemblies with an N50 > 10000"/>
15f6ef1d7c96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
iuc
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40 <param name="emb_comebin" type="integer" value="2048" label="Embedding size for COMEBin network"/>
15f6ef1d7c96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
iuc
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41 <param name="emb_cov" type="integer" value="2048" label="Embedding size for coverage network"/>
15f6ef1d7c96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
iuc
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42 <param name="batch" type="integer" value="1024" label="Batch size"/>
0
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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43 </inputs>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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44 <outputs>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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45 <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS">
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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46 <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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47 </collection>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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48 </outputs>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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49 <tests>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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50 <test expect_exit_code="1" expect_failure="true">
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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51 <param name="assembly_file" ftype="fasta" value="input_single.fasta"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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52 <param name="bam_files" ftype="bam" value="input_single.bam"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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53 <param name="learning" value="6"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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54 <param name="loss" value="0.15"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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55 <param name="emb_comebin" value="2048"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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56 <param name="emb_cov" value="2048"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
iuc
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57 <param name="batch" value="1024"/>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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58 </test>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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59 </tests>
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60 <help>
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61 <![CDATA[
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62
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63 **IMPORTANT**
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64
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65 It might happen that this tool will throw out an error. If this error happen: ValueError: max() arg is an empty sequence
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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66 then try to run this tool with different values it might fix this. When this error happen: UnboundLocalError: local variable 'logits' referenced before assignment
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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67 then the imputed data might not be enough such that this tool will function correctly.
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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68
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69 Also the run-time of this tool will be high since it is machining learning tool for binning!
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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70
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71 **Input**
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72
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73 - The assembly file in fasta format
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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74 - The corresponded bam file(s) to the assembly file
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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75
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76 **Output**
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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77
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78 As output from the tool is a collection of bins created with machining learning
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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79
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81 ]]>
2576c9132481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit 392e72b84376b11b19759ba85261d99f05c4f64e
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82 </help>
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83 <expand macro="citations"/>
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84 </tool>