annotate bionano_scaffold.xml @ 11:3371c5bdc17a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f2952aec50c8bf269f95bd3caa634b232e640729
author bgruening
date Mon, 27 Feb 2023 14:32:45 +0000
parents 22286dab5aa1
children
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1 <tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>automates the scaffolding process</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set RefAligner = '/RefAligner/RefAligner'
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10 #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta'
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11 #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta'
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12 ## softlinks do not work
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13 cp '${ngs_fasta}' ./ngs.fasta
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14 && cp '${bionano_cmap}' ./bionano.cmap
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15 && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024))
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16 ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots
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17 && export SLOTS=\$(( \${GALAXY_SLOTS:-2} > 2 ? \${GALAXY_SLOTS:-2} : 2 ))
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18 #if $configuration_options.configuration == 'vgp'
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19 && cp '${vgp_mode}' ./config.xml
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20 && sed -i "s|__MEMORY__|\$GALAXY_MEMORY_GB|" ./config.xml
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21 && sed -i "s|__CORES__|\$SLOTS|" ./config.xml
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22 #else
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23 && cp '${configuration_file}' ./config.xml
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24 && sed -i "s|attr=\"maxmem\" val0=.* display|attr=\"maxmem\" val0=\"\$GALAXY_MEMORY_GB\" display|" ./config.xml
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25 && sed -i "s|attr=\"maxthreads\" val0=.* display|attr=\"maxthreads\" val0=\"\$SLOTS\" display|" ./config.xml
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26 && sed -i "s|attr=\"maxvirtmem\" val0=.*/>|attr=\"maxvirtmem\" val0=\"\$GALAXY_MEMORY_GB\"/>|" ./config.xml
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27 && sed -i "s|attr=\"insertThreads\" val0=.*/>|attr=\"insertThreads\" val0=\"\$SLOTS\"/>|" ./config.xml
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28 #end if
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29 ## output the configuration file on stdout
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30 && cat ./config.xml
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31 && perl '/HybridScaffold/hybridScaffold.pl'
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32 -n ./ngs.fasta
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33 -b ./bionano.cmap
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34 -c ./config.xml
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35 -r $RefAligner
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36 #if $conflict_resolution
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37 -M '${conflict_resolution}'
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38 #else
1
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39 -B $conflict_filter_genome
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40 -N $conflict_filter_sequence
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41 #end if
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42 ##$align_molecules_options.align_molecules
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43 ###if $align_molecules_options.align_molecules
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44 ## -m $align_molecules_options.bionano_molecules
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45 ## -q '${align_molecules_options.optarguments_xml}'
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46 ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/
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47 ###end if
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48 ##$quimeric_quality_options.quimeric_quality
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49 ###if $quimeric_quality_options.quimeric_quality
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50 ## -m $align_molecules_options.bionano_molecules
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51 ## #if $quimeric_quality_conditional.noise_parameter
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52 ## -e '${quimeric_quality_conditional.noise_parameter}'
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53 ## #end if
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54 ###end if
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55 -f
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56 $zip_file
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57 -o ./
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58 #if $trim_cut_sites
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59 && export PATH=/opt/conda/bin/:\$PATH
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60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
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61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
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62 #end if
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63 ## the next lines are required because the XXXX_cut.txt file is not always generated
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64 && touch hybrid_scaffolds/temp_cut.txt
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65 && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt
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66 ]]> </command>
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67 <configfiles>
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68 <configfile name="vgp_mode"><![CDATA[
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69 #if $configuration_options.configuration == 'vgp'
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70 <hybridScaffold>
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71 <version>
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72 <flag attr="version" val0="\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \$"/>
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73 </version>
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74 <global>
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75 <flag attr="maxmem" val0="__MEMORY__" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
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76 <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
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77 <flag attr="maxvirtmem" val0="__MEMORY__"/>
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78 <flag attr="RAmem" val0="3" val1="1"/>
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79 </global>
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80 <fasta2cmap>
4
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81 <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
1
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82 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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83 <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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84 <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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85 </fasta2cmap>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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86 <align0>
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87 <flag attr="M" val0="1" val1="3"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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88 <flag attr="ScaleDelta" val0="0.02" val1="15"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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89 <flag attr="ScaleDeltaBPP"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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90 <flag attr="hashScaleDelta" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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91 <flag attr="res" val0="2.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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92 <flag attr="FP" val0="0.6"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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93 <flag attr="FN" val0="0.06"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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94 <flag attr="sf" val0="0.20"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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95 <flag attr="sd" val0="0.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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96 <flag attr="sr" val0="0.01"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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97 <flag attr="extend" val0="1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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98 <flag attr="outlier" val0="0.0001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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99 <flag attr="endoutlier" val0="0.001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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100 <flag attr="PVendoutlier"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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101 <flag attr="deltaX" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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102 <flag attr="deltaY" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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103 <flag attr="xmapchim" val0="12"/>
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104 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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105 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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106 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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107 <flag attr="insertThreads" val0="__CORES__"/>
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108 <flag attr="nosplit" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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109 <flag attr="biaswt" val0="0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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110 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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111 <flag attr="S" val0="-1000"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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112 <flag attr="indel"/>
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113 <flag attr="PVres" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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114 <flag attr="rres" val0="0.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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115 <flag attr="MaxSE" val0="0.5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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116 <flag attr="HSDrange" val0="1.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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117 <flag attr="outlierBC"/>
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118 <flag attr="xmapUnique" val0="12"/>
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119 <flag attr="AlignRes" val0="2."/>
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120 <flag attr="outlierExtend" val0="12" val1="24"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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121 <flag attr="Kmax" val0="12"/>
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122 <flag attr="resEstimate"/>
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123 <flag attr="f"/>
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124 <flag attr="mres" val0="0.9"/>
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125 </align0>
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126 <align1>
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127 <flag attr="res" val0="2.9"/>
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128 <flag attr="FP" val0="0.6"/>
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129 <flag attr="FN" val0="0.06"/>
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130 <flag attr="sf" val0="0.20"/>
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131 <flag attr="sd" val0="0.0"/>
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132 <flag attr="sr" val0="0.01"/>
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133 <flag attr="extend" val0="1"/>
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134 <flag attr="outlier" val0="0.0001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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135 <flag attr="endoutlier" val0="0.001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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136 <flag attr="PVendoutlier"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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137 <flag attr="deltaX" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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138 <flag attr="deltaY" val0="12"/>
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139 <flag attr="xmapchim" val0="12"/>
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140 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
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141 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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142 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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143 <flag attr="insertThreads" val0="__CORES__"/>
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144 <flag attr="nosplit" val0="2"/>
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145 <flag attr="biaswt" val0="0"/>
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146 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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147 <flag attr="S" val0="-1000"/>
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148 <flag attr="indel"/>
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149 <flag attr="PVres" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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150 <flag attr="rres" val0="0.9"/>
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151 <flag attr="MaxSE" val0="0.5"/>
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152 <flag attr="HSDrange" val0="1.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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153 <flag attr="outlierBC"/>
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154 <flag attr="xmapUnique" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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155 <flag attr="AlignRes" val0="2."/>
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156 <flag attr="outlierExtend" val0="12" val1="24"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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157 <flag attr="Kmax" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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158 <flag attr="resEstimate"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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159 <flag attr="f"/>
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160 <flag attr="mres" val0="0.9"/>
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161 </align1>
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162 <assignAlignType>
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163 <flag attr="T_cutoff" val0="1e-11" display="P-value" group="Chimeric/conflicting alignment flagging" description="Minimum confidence value used to flag chimeric/conflicting alignments. Recommand to set it to be the same as the merge_Tvalue below."/>
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164 <flag attr="max_overhang" val0="5" display=""/>
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165 </assignAlignType>
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166 <cut_conflicts>
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167 <flag attr="window_size" val0="10000" display="Distance (bp)" group="Conflict-cut" description="The distance (bp) from a conflicting site within which the chimeric quality score of BioNano genome map labels will be examined"/>
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168 <flag attr="min_quality_score_threshold" val0="35" display="Percent (%)" group="Conflict-cut" description="The minimal percentage of molecules spanning to the left and right of a label of interest, thus supporting the BioNano assembly at that region"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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169 <flag attr="min_coverage_threshold" val0="10" display="Coverage (X)" group="Conflict-cut" description="The minimal number of molecules aligning to a label of interest in the BioNano assembly"/>
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170 </cut_conflicts>
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171 <mergeNGS_BN>
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172 <flag attr="merge_Tvalue" val0="1e-11" display="P-value" group="Merging" description="Minimum confidence value used to merge alignments. Recommand to set it to be the same as the assignAlignType T_cutoff above"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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173 <flag attr="id_shift" val0="100000" display="BioNano cmap id shift" group="Merging" description="Value to shift the BioNano cmap id to distinguish the BioNano cmaps from sequence cmaps. Recommand to set it to be greater than the number of sequence entries."/>
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174 <flag attr="max_merge_rounds" val0="40" display=""/>
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175 <flag attr="endoutlier" val0="1e-4" display=""/>
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176 <flag attr="outlier" val0="1e-4" display=""/>
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177 <flag attr="biaswt" val0="0" display=""/>
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178 <flag attr="sd" val0="0.1" display=""/>
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179 <flag attr="res" val0="2.9" display=""/>
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180 <flag attr="mres" val0="2.9" display=""/>
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181 <flag attr="sf" val0="0.2" display=""/>
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182 <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
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183 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
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184 <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
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185 <flag attr="maxmem" val0="__MEMORY__" display=""/>
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186 <flag attr="pairmergeRepeat"/>
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187 <flag attr="NoBpp"/>
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188 <flag attr="first" val0="-1" display=""/>
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189 <flag attr="f"/>
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190 </mergeNGS_BN>
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191 <align_final_1st_pass>
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192 <flag attr="res" val0="2.9"/>
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193 <flag attr="FP" val0="0.6"/>
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194 <flag attr="FN" val0="0.06"/>
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195 <flag attr="sf" val0="0.20"/>
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196 <flag attr="sd" val0="0.0"/>
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197 <flag attr="sr" val0="0.01"/>
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198 <flag attr="extend" val0="1"/>
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199 <flag attr="outlier" val0="0.0001"/>
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200 <flag attr="endoutlier" val0="0.001"/>
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201 <flag attr="PVendoutlier"/>
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202 <flag attr="deltaX" val0="12"/>
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203 <flag attr="deltaY" val0="12"/>
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204 <flag attr="xmapchim" val0="12"/>
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205 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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206 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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207 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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295c0e28f4ee "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3"
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208 <flag attr="insertThreads" val0="__CORES__"/>
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209 <flag attr="nosplit" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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210 <flag attr="biaswt" val0="0"/>
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211 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
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212 <flag attr="S" val0="-1000"/>
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213 <flag attr="indel"/>
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214 <flag attr="PVres" val0="2"/>
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215 <flag attr="rres" val0="0.9"/>
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216 <flag attr="MaxSE" val0="0.5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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217 <flag attr="HSDrange" val0="1.0"/>
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218 <flag attr="outlierBC"/>
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219 <flag attr="xmapUnique" val0="12"/>
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220 <flag attr="AlignRes" val0="2."/>
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221 <flag attr="outlierExtend" val0="6" val1="24"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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222 <flag attr="Kmax" val0="6"/>
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223 <flag attr="resEstimate"/>
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224 <flag attr="f"/>
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225 <flag attr="mres" val0="0.9"/>
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226 <flag attr="MultiMatches" val0="5"/>
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227 </align_final_1st_pass>
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228 <align_final_2nd_pass>
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229 <flag attr="res" val0="2.9"/>
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230 <flag attr="FP" val0="0.6"/>
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231 <flag attr="FN" val0="0.06"/>
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232 <flag attr="sf" val0="0.20"/>
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233 <flag attr="sd" val0="0.0"/>
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234 <flag attr="sr" val0="0.01"/>
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235 <flag attr="extend" val0="1"/>
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236 <flag attr="outlier" val0="0.0001"/>
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237 <flag attr="endoutlier" val0="0.001"/>
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238 <flag attr="PVendoutlier"/>
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239 <flag attr="deltaX" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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240 <flag attr="deltaY" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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241 <flag attr="xmapchim" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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242 <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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243 <flag attr="hash" val0="-hashdelta" val1="50"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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244 <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
3
295c0e28f4ee "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3"
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245 <flag attr="insertThreads" val0="__CORES__"/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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246 <flag attr="nosplit" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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247 <flag attr="biaswt" val0="0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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248 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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249 <flag attr="S" val0="-1000"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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250 <flag attr="indel"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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251 <flag attr="PVres" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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252 <flag attr="rres" val0="0.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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253 <flag attr="MaxSE" val0="0.5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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254 <flag attr="HSDrange" val0="1.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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255 <flag attr="outlierBC"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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256 <flag attr="xmapUnique" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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257 <flag attr="AlignRes" val0="2."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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258 <flag attr="outlierExtend" val0="12" val1="24"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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259 <flag attr="Kmax" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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260 <flag attr="resEstimate"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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261 <flag attr="f"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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262 <flag attr="mres" val0="0.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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263 <flag attr="MultiMatches" val0="5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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264 </align_final_2nd_pass>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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265 <align_final_BNG>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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266 <flag attr="res" val0="2.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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267 <flag attr="FP" val0="0.6"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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268 <flag attr="FN" val0="0.06"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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269 <flag attr="sf" val0="0.20"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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270 <flag attr="sd" val0="0.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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271 <flag attr="sr" val0="0.01"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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272 <flag attr="extend" val0="1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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273 <flag attr="outlier" val0="0.0001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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274 <flag attr="endoutlier" val0="0.001"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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275 <flag attr="PVendoutlier"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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276 <flag attr="deltaX" val0="6"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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277 <flag attr="deltaY" val0="6"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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278 <flag attr="xmapchim" val0="12"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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279 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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280 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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281 <flag attr="hashMultiMatch" val0="30" val1="10"/>
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295c0e28f4ee "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3"
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282 <flag attr="insertThreads" val0="__CORES__"/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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283 <flag attr="nosplit" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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284 <flag attr="biaswt" val0="0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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285 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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286 <flag attr="S" val0="-1000"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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287 <flag attr="indel"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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288 <flag attr="PVres" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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289 <flag attr="rres" val0="0.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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290 <flag attr="MaxSE" val0="0.5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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291 <flag attr="HSDrange" val0="1.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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292 <flag attr="outlierBC"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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293 <flag attr="xmapUnique" val0="14"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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294 <flag attr="AlignRes" val0="2."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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295 <flag attr="outlierExtend" val0="6" val1="24"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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296 <flag attr="Kmax" val0="6"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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297 <flag attr="resEstimate"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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298 <flag attr="BestRef" val0="1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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299 <flag attr="f"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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300 <flag attr="mres" val0="0.9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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301 </align_final_BNG>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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302 <refineFinal1>
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303 <flag attr="refine" val0="1" display="Refine Map" group="Final Refinement" default0="3"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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304 <flag attr="usecolor" val0="1" default0="1" display="Color Channel" group="Final Refinement"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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305 <flag attr="A" val0="5" display="Aligned Sites Threshold" group="Final Refinement" default0="5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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306 <flat attr="S" val0="-9"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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307 <flag attr="L" val0="130"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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308 <flag attr="maptype" val0="0"/>
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309 <flag attr="extend" val0="1" display="Allow Extended Molecule" group="Final Refinement" default0="1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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310 <flag attr="MaxCov" val0="100" display="Max Coverage" group="Final Refinement" default0="100"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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311 <flag attr="Mprobeval" display="Fast Mode" group="Final Refinement"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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312 <flag attr="splitcnt"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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313 <flag attr="splitrev" val0="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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314 <flag attr="CmapSNR"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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315 <flag attr="splitsite"/>
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316 <flag attr="MinSplitLen" val0="50.0"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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317 <flag attr="MaxSE" val0="0.5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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318 <flag attr="outlier" val0="2e-2" display="Min Outliers P-value" group="Second Refinement" default0="1e-5"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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319 <flag attr="outlierMax" val0="80."/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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320 <flag attr="outlierLambda" val0="20."/>
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321 <flag attr="endoutlier" val0="1e-3" display="Molecule Ends P-value Cutoff" group="Second Refinement" default0="1e-4"/>
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322 <flag attr="endoutlierRef" val0="1e-4" val1="1e-3"/>
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323 <flag attr="skip_dist" val0="0.0" val2="0.0"/>
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324 <flag attr="endoutlierFinal" val0="1"/>
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325 <flag attr="maxEnd" val0="90."/>
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326 <flag attr="RTHETA_FIX" val0="0"/>
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327 <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/>
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328 <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/>
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329 <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/>
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330 <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/>
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331 <flag attr="biaswtEnd" val0="0.0"/>
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332 <flag attr="biaswtRefine" val0="0.7" val2="1"/>
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333 <flag attr="biaswtOutlier" val0="0.0"/>
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334 <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/>
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335 <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/>
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336 <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/>
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337 <flag attr="RepeatMask" val0="5" val1="0.01" display="Repeat Mask P-values" group="Final Refinement" default0="2" default1="0.01"/>
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338 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/>
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339 <flag attr="CovTrim" val0="2"/>
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340 <flag attr="CovTrimLen" val0="55"/>
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341 <flag attr="TrimNorm" val0="0"/>
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342 <flag attr="TrimNormMed" val0="100"/>
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343 <flag attr="TrimNormChim" val0="2"/>
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344 <flag attr="TrimNormMin" val0="2"/>
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345 <flag attr="PVres" val0="2"/>
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346 <flag attr="PVendoutlier"/>
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347 <flag attr="AlignRes" val0="1.5"/>
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348 <flag attr="rres" val0="1.2"/>
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349 <flag attr="cres" val0="5.6" val1="3" val2="0.1"/>
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350 <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/>
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351 <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>
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352 <flag attr="HSDrange" val0="1.0"/>
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353 <flag attr="hashoffset" val0="1"/>
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354 <flag attr="hashMultiMatch" val0="15"/>
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355 <flag attr="insertThreads" val0="__CORES__"/>
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356 <flag attr="BestRef" val0="1"/>
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357 <flag attr="BestRefPV" val0="1"/>
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358 <flag attr="ChimQuality"/>
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359 <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>
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360 <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>
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361 </refineFinal1>
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362 </hybridScaffold>
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363 #end if
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364 ]]></configfile>
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365 </configfiles>
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366 <inputs>
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367 <param name="ngs_fasta" argument="-n" type="data" format="fasta" label="NGS FASTA" help="Input NGS FASTA"/>
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368 <param name="bionano_cmap" argument="-b" type="data" format="cmap" label="BioNano CMAP" help="Input BioNano CMAP"/>
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369 <conditional name="configuration_options">
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370 <param name="configuration" argument="-c" type="select" label="Configuration mode" help="It defines the parameters used in each step of hybrid scaffold">
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371 <option value="vgp">VGP mode</option>
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372 <option value="file">Select a configuration file</option>
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373 </param>
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374 <when value="vgp">
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375 <param name="enzyme" type="text" value="CTTAAG" label="Restriction enzyme" help="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1.">
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376 <expand macro="sanitize_string" />
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377 </param>
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378 </when>
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379 <when value="file">
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380 <param name="configuration_file" type="data" format="xml,txt" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/>
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381 </when>
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382 </conditional>
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383 <param name="conflict_resolution" argument="-M" type="data" format="txt" optional="True" label="Conflict resolution file" help="Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]"/>
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384 <param name="conflict_filter_genome" argument="-B" type="select" label="Genome maps conflict filter" help="Conflict filter level genome maps [required if not using -M option]">
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385 <option value="1">No filter</option>
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386 <option value="2">Cut contig at conflict</option>
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387 <option value="3">Exclude conflicting contig</option>
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388 </param>
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389 <param name="conflict_filter_sequence" argument="-N" type="select" label="Sequences conflict filter" help="Conflict filter level for sequences [required if not using -M option]">
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390 <option value="1">No filter</option>
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391 <option value="2">Cut contig at conflict</option>
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392 <option value="3">Exclude conflicting contig</option>
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393 </param>
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394 <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide BisCot required files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" />
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395 <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" />
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396 <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." />
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397 <!--
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398
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399 Those options have been disabled because the Docker container doesn't include the required packages
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400
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401 <conditional name="align_molecules_options">
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402 <param name="align_molecules" type="select" label="Align molecules to hybrid scaffolds and genome maps" help="Flag to generate molecules to hybrid scaffold alignment and molecules to genome map alignment">
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403 <option value="-x">True</option>
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404 <option value="" selected="True">False</option>
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405 </param>
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406 <when value="-x">
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407 <param name="bionano_molecules" type="data" format="bnx" label="Bionano molecules" help="Input BioNano molecules BNX [optional; only required for either the -x or -y option]"/>
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408 <param name="optarguments_xml" type="data" format="xml" label="OptArguments XML script" help="Input de novo assembly pipeline optArguments XML script [optional; only required for -x option]"/>
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409 </when>
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410 <when value="">
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411 </when>
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412 </conditional>
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413 <conditional name="quimeric_quality_options">
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414 <param name="quimeric_quality" type="select" label="Generate quimeric quality score" help="Flag to generate chimeric quality score for the Input BioNano CMAP">
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415 <option value="-y">True</option>
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416 <option value="" selected="True">False</option>
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417 </param>
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418 <when value="-y">
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419 <param name="bionano_molecules" type="data" format="bnx" label="Bionano molecules" help="Input BioNano molecules BNX [optional; only required for either the -x or -y option]"/>
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420 <param name="noise_parameter" type="data" format="txt" optional="True" label="Noise parameter file" help="Input de novo assembly noise parameter .errbin or .err file [optional; recommended for -y option but not required]"/>
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421 </when>
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422 <when value="">
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423 </when>
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424 </conditional>
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425 -->
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426 </inputs>
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427 <outputs>
5
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428 <data name="ngs_contigs_scaffold" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI">
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429 <filter>trim_cut_sites == False</filter>
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430 </data>
5
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431 <data name="ngs_contigs_not_scaffolded" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded">
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432 <filter>trim_cut_sites == False</filter>
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433 </data>
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434 <data name="ngs_contigs_scaffold_trimmed" format="fasta" from_work_dir="SCAFFOLD_NCBI_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI trimmed">
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435 <filter>trim_cut_sites</filter>
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436 </data>
5
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437 <data name="ngs_contigs_not_scaffolded_trimmed" format="fasta" from_work_dir="NOT_SCAFFOLDED_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded trimmed">
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438 <filter>trim_cut_sites</filter>
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439 </data>
1
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440 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>
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441 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
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442 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
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443 <filter>zip_file</filter>
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444 </data>
6
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445 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
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446
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447 <data name="query_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap" label="${tool.name} on ${on_string}: query CMAP">
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448 <filter>all_files</filter>
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449 </data>
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450 <data name="reference_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_r.cmap" label="${tool.name} on ${on_string}: reference CMAP">
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451 <filter>all_files</filter>
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452 </data>
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453 <data name="xmap_file" format="xml" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap" label="${tool.name} on ${on_string}: XMAP configuration">
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454 <filter>all_files</filter>
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455 </data>
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456 <data name="key_file" format="tabular" from_work_dir="hybrid_scaffolds/keys.txt" label="${tool.name} on ${on_string}: Bionano key file">
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457 <filter>all_files</filter>
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458 </data>
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459 </outputs>
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460 <tests>
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461 <test expect_num_outputs="6">
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462 <param name="ngs_fasta" value="assembly.fasta.gz"/>
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463 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
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464 <param name="conflict_filter_genome" value="3"/>
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465 <param name="conflict_filter_sequence" value="3"/>
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466 <conditional name="configuration_options">
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467 <param name="configuration" value="file"/>
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468 <param name="configuration_file" value="configuration.xml"/>
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469 </conditional>
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470 <param name="zip_file" value="true"/>
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471 <param name="trim_cut_sites" value="false"/>
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472 <output name="ngs_contigs_scaffold" ftype="fasta">
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473 <assert_contents>
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474 <has_size value="4753369" delta="100" />
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475 <has_n_lines n="2"/>
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diff changeset
476 <has_line line=">Super-Scaffold_1"/>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
477 </assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
478 </output>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
479 <output name="report" file="test_01_report.txt" ftype="txt"/>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
480 <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
481 <output name="conflicts" ftype="txt">
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
482 <assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
483 <has_text text="alignmentOrientation" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
484 </assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
485 </output>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
486 <output name="results" ftype="zip">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
487 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
488 <has_archive_member path=".*/status.txt"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
489 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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diff changeset
490 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
491 <assert_stdout>
7
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
492 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
493 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
494 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
495 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
496 <has_text text="hybridScaffold"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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diff changeset
497 </assert_stdout>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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diff changeset
498 </test>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
499 <test expect_num_outputs="5">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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diff changeset
500 <param name="ngs_fasta" value="assembly.fasta.gz"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
501 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
502 <param name="conflict_filter_genome" value="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
503 <param name="conflict_filter_sequence" value="2"/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
504 <param name="trim_cut_sites" value="false"/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
505 <conditional name="configuration_options">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
506 <param name="configuration" value="file"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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diff changeset
507 <param name="configuration_file" value="configuration.xml"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
508 </conditional>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
509 <output name="ngs_contigs_scaffold" ftype="fasta">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
510 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
511 <has_size value="4753369" delta="100" />
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
512 <has_n_lines n="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
513 <has_line line=">Super-Scaffold_1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
514 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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diff changeset
515 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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diff changeset
516 <output name="report" file="test_02_report.txt" ftype="txt"/>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
517 <output name="ngs_contigs_scaffold_agp" ftype="agp">
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
518 <assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
519 <has_size value="311" delta="20" />
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
520 <has_text text="##agp-version"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
521 <has_n_lines n="9"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
522 </assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
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parents: 5
diff changeset
523 </output>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
524 <output name="conflicts" ftype="txt">
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
525 <assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
526 <has_text text="alignmentOrientation" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
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parents: 4
diff changeset
527 </assert_contents>
9
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
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parents: 8
diff changeset
528 </output>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
529 <assert_stdout>
9
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
530 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
531 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
7
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
532 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
533 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
534 <has_text text="hybridScaffold"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
535 </assert_stdout>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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parents:
diff changeset
536 </test>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
537 <test expect_num_outputs="6">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
538 <param name="ngs_fasta" value="assembly.fasta.gz"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
539 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
540 <param name="conflict_filter_genome" value="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
541 <param name="conflict_filter_sequence" value="3"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
542 <conditional name="configuration_options">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
543 <param name="configuration" value="file"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
544 <param name="configuration_file" value="configuration.xml"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
545 </conditional>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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parents:
diff changeset
546 <param name="zip_file" value="true"/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
547 <param name="trim_cut_sites" value="false"/>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
548 <output name="ngs_contigs_scaffold" ftype="fasta">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
549 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
550 <has_size value="4753369" delta="100" />
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
551 <has_n_lines n="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
552 <has_line line=">Super-Scaffold_1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
553 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
554 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
555 <output name="report" file="test_03_report.txt" ftype="txt"/>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
556 <output name="ngs_contigs_scaffold_agp" ftype="agp">
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
557 <assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
558 <has_size value="311" delta="20" />
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
559 <has_text text="##agp-version"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
560 <has_n_lines n="9"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
561 </assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
562 </output>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
563 <output name="conflicts" ftype="txt">
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
564 <assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
565 <has_text text="alignmentOrientation" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
566 </assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
567 </output>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
568 <output name="results" ftype="zip">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
569 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
570 <has_archive_member path=".*/status.txt"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
571 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
572 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
573 <assert_stdout>
7
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
574 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
575 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
576 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
577 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
578 <has_text text="hybridScaffold"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
579 </assert_stdout>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
580 </test>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
581 <test expect_num_outputs="6">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
582 <param name="ngs_fasta" value="assembly.fasta.gz"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
583 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
584 <param name="conflict_filter_genome" value="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
585 <param name="conflict_filter_sequence" value="3"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
586 <conditional name="configuration_options">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
587 <param name="configuration" value="vgp"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
588 <param name="enzyme" value="BspQI"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
589 </conditional>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
590 <param name="zip_file" value="true"/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
591 <param name="trim_cut_sites" value="false"/>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
592 <output name="ngs_contigs_scaffold" ftype="fasta">
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
593 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
594 <has_size value="4753369" delta="100" />
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
595 <has_n_lines n="2"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
596 <has_line line=">Super-Scaffold_1"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
597 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
598 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
599 <output name="report" file="test_04_report.txt" ftype="txt"/>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
600 <output name="ngs_contigs_scaffold_agp" ftype="agp">
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
601 <assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
602 <has_size value="311" delta="20" />
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
603 <has_text text="##agp-version"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
604 <has_n_lines n="9"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
605 </assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
606 </output>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
607 <output name="conflicts" ftype="txt">
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
608 <assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
609 <has_text text="alignmentOrientation" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
610 </assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
611 </output>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
612 <output name="results" ftype="zip">
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
613 <assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
614 <has_archive_member path=".*/status.txt"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
615 </assert_contents>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
616 </output>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
617 <assert_stdout>
7
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
618 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
619 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
620 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
621 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
622 <has_text text="hybridScaffold"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
623 </assert_stdout>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
624 </test>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
625 <test expect_num_outputs="5">
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
626 <param name="ngs_fasta" value="assembly.fasta.gz"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
627 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
628 <param name="conflict_filter_genome" value="3"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
629 <param name="conflict_filter_sequence" value="3"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
630 <conditional name="configuration_options">
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
631 <param name="configuration" value="file"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
632 <param name="configuration_file" value="configuration.xml"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
633 </conditional>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
634 <param name="trim_cut_sites" value="true"/>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
635 <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
636 <assert_contents>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
637 <has_size value="4832591" delta="100" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
638 <has_n_lines n="79224"/>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
639 <has_line line=">Super-Scaffold_1"/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
640 </assert_contents>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
641 </output>
9
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
642 <output name="conflicts" ftype="txt">
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
643 <assert_contents>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
644 <has_text text="alignmentOrientation" />
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
645 </assert_contents>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
646 </output>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
647 <output name="report" file="test_05_report.txt" ftype="txt"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
648 <output name="ngs_contigs_scaffold_agp" ftype="agp">
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
649 <assert_contents>
9
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
650 <has_size value="311" delta="20" />
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
651 <has_text text="##agp-version"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
652 <has_n_lines n="9"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
653 </assert_contents>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
654 </output>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
655 <assert_stdout>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
656 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
657 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
658 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
659 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
660 <has_text text="hybridScaffold"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
661 </assert_stdout>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
662 </test>
10
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
663 <test expect_num_outputs="9">
9
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
664 <param name="ngs_fasta" value="assembly.fasta.gz"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
665 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
666 <param name="conflict_filter_genome" value="3"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
667 <param name="conflict_filter_sequence" value="3"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
668 <param name="all_files" value="true"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
669 <conditional name="configuration_options">
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
670 <param name="configuration" value="file"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
671 <param name="configuration_file" value="configuration.xml"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
672 </conditional>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
673 <param name="trim_cut_sites" value="true"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
674 <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
675 <assert_contents>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
676 <has_size value="4832591" delta="100" />
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
677 <has_n_lines n="79224"/>
faee8629b460 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
bgruening
parents: 8
diff changeset
678 <has_line line=">Super-Scaffold_1"/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
679 </assert_contents>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
680 </output>
5
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
681 <output name="conflicts" ftype="txt">
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
682 <assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
683 <has_text text="alignmentOrientation" />
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
684 </assert_contents>
96cacb31d571 "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
bgruening
parents: 4
diff changeset
685 </output>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
686 <output name="report" file="test_05_report.txt" ftype="txt"/>
6
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
687 <output name="ngs_contigs_scaffold_agp" ftype="agp">
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
688 <assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
689 <has_size value="311" delta="20" />
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
690 <has_text text="##agp-version"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
691 <has_n_lines n="9"/>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
692 </assert_contents>
5d7c5ae1b69b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
bgruening
parents: 5
diff changeset
693 </output>
10
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
694 <output name="query_file" ftype="cmap">
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
695 <assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
696 <has_text text="3879935.1"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
697 <has_text text="Coverage refer to the interval between current site and next site"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
698 </assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
699 </output>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
700 <output name="reference_file" ftype="cmap">
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
701 <assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
702 <has_text text="4753350.0"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
703 <has_text text=" StdDev refers to the interval between the current site and the next site"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
704 </assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
705 </output>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
706 <output name="xmap_file" ftype="xml">
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
707 <assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
708 <has_text text="XMAP File Version"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
709 <has_text text="(7,7)(8,8)(9,9)(10,10)(11,11)(12,12)(13,13)"/>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
710 </assert_contents>
22286dab5aa1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
bgruening
parents: 9
diff changeset
711 </output>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
712 <assert_stdout>
7
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
713 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
714 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
715 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
a7f16f24e9a1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bcbd45152c1809e656b2d09187847608a606d02c"
bgruening
parents: 6
diff changeset
716 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
717 <has_text text="hybridScaffold"/>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
718 </assert_stdout>
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
bgruening
parents: 3
diff changeset
719 </test>
1
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
720 </tests>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
721 <help><![CDATA[
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
722 .. class:: infomark
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
723
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
724 **Purpose**
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
725
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
726 The Hybrid Scaffold pipeline automates the comprehensive scaffolding process and is consisted of five major steps: 1) generate in silico maps for sequence assembly; 2) align in silico sequence maps against Bionano genome maps to identify and resolve potential conflicts in either data set; 3) merge the non-conflicting maps into hybrid scaffolds; 4) align sequence maps to the hybrid scaffolds; and 5) generate AGP and FASTA files for the scaffolds.
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
727
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
728 ----
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
729
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
730 .. class:: infomark
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
731
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
732 **Coverage**
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
733
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
734 For Hybrid Scaffold, we recommend using as input a minimum of 80X effective molecule coverage in order to build an accurate and contiguous consensus genome map assembly for each enzyme. When using nickases, using more coverage does not significantly improve map contiguity. When using a DLS enzyme such as DLE-1, effective coverage up to and beyond 100X has shown improved map contiguities for some plants and animals.
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
parents:
diff changeset
735
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
bgruening
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736 ----
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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737
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738 .. class:: infomark
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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739
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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740 **Input Bionano assembly**
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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741
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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742 When running the de novo assembly pipeline for hybrid scaffolding applications, users are recommended to use assembly parameters for non-haplotype-aware assembly. The current Hybrid Scaffold pipeline does not explicitly handle haplotype information and assumes there is only one genome map or NGS sequence contig covering a given genomic region. If multiple haplotypes are present, the pipeline may make false positive conflict cuts and incorrectly mix haplotypes in the final scaffolds. We understand that haplotype information is important in many applications, and a fully haplotype-aware Hybrid Scaffold pipeline is in our roadmap for a future release.
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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743
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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744 ----
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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745
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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746 .. class:: infomark
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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747
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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748 @BIONANO_SUPPORT_TEXT@
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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749
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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750 ]]> </help>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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751 <expand macro="citations"/>
9bd94d9a1b2e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
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752 </tool>