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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"
author iuc
date Tue, 16 Nov 2021 19:57:38 +0000
parents 36093854bfc7
children
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36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1">
0
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2 <description>Transposable Element Typer</description>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1</token>
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5 </macros>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement>
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8 </requirements>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 ## avoid creating indices in the inputdir
edcf603bedfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"
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12 ln -s '$reference' reference.fa &&
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13 TETyper.py
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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14 --threads \${GALAXY_SLOTS:-1}
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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15 #if $collection_paired.selector == "paired"
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16 --fq1 '${collection_paired.forward_input}' --fq2 '${collection_paired.reverse_input}'
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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17 #elif $collection_paired.selector == "collection":
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18 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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19 #end if
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20 --ref 'reference.fa'
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21 --flank_len '${flank_length}'
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22 --min_reads '${min_reads}'
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23 --min_each_strand '${min_each_strand}'
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24 --min_mapped_len '${min_mapped_len}'
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25 --min_qual '${min_qual}'
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26 #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table":
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27 --snp_profiles '$snp_profiles_source.snp_profiles.fields.path'
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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28 #elif str( $snp_profiles_source.snp_profiles_source_selector ) == 'history':
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29 --snp_profiles '$snp_profiles_source.snp_profiles'
0
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30 #end if
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31 #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table":
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32 --struct_profiles '$struct_profiles_source.struct_profiles.fields.path'
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33 #elif str( $struct_profiles_source.struct_profiles_source_selector ) == 'history':
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34 --struct_profiles '$struct_profiles_source.struct_profiles'
0
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35 #end if
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36 --outprefix output
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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37 ]]>
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38 </command>
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39 <inputs>
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40 <conditional name="collection_paired">
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41 <param name="selector" type="select" label="Collection or paired reads" >
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42 <option value="collection">Collection</option>
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43 <option value="paired" selected="True">Paired</option>
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44 </param>
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45 <when value="collection">
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46 <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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47 </when>
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48 <when value="paired">
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49 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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50 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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51 </when>
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52 </conditional>
1
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53 <conditional name="snp_profiles_source">
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54 <param name="snp_profiles_source_selector" type="select"
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55 label="Select a SNP profile from your history or use one from a tool data table?">
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56 <option value="No" selected="true">No SNP profile</option>
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57 <option value="tool_data_table">SNP profile from tool data table</option>
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58 <option value="history">SNP profile from history</option>
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59 </param>
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60 <when value="No"/>
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61 <when value="tool_data_table">
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62 <param name="snp_profiles" type="select" format="tabular" label="SNP Profile">
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63 <options from_data_table="tetyper_snp_profiles">
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64 <validator type="no_options" message="No TETyper SNP profiles are available" />
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65 </options>
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66 </param>
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67 </when>
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68 <when value="history">
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69 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile"
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70 help="A three-column tabular file with SNP profile definitions"/>
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71 </when>
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72 </conditional>
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73 <conditional name="struct_profiles_source">
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74 <param name="struct_profiles_source_selector" type="select"
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75 label="Select a structural variant profile from your history or use one from a tool data table?">
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76 <option value="No" selected="true">No structural variant profile</option>
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77 <option value="tool_data_table">Structural variant profile from tool data table</option>
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78 <option value="history" selected="true">Structural variant profile from history</option>
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79 </param>
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80 <when value="No"/>
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81 <when value="tool_data_table">
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82 <param name="struct_profiles" type="select" format="tabular"
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parents: 0
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83 label="Structural Variant Profile">
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84 <options from_data_table="tetyper_struct_profiles">
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parents: 0
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85 <validator type="no_options" message="No TETyper structural variant profiles are available" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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parents: 0
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86 </options>
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87 </param>
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88 </when>
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parents: 0
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89 <when value="history">
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90 <param name="struct_profiles" type="data" format="tabular"
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91 label="Structural Variant Profile"
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92 help="A two-column tabular file with structural variant profile definitions"/>
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93 </when>
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94 </conditional>
0
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95 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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96 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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97 <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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98 <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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99 <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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100 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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101 <param name="include_log" type="boolean" label="Include log in output"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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102 </inputs>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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103 <outputs>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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104 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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105 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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106 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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107 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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108 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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109 <filter>include_log</filter>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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110 </data>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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111 </outputs>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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112 <tests>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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113 <test>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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114 <param name="reference" value="Tn4401b-1.fasta" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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115 <conditional name="collection_paired">
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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116 <param name="selector" value="paired" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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117 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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118 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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119 </conditional>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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120 <output name="summary" file="output_summary_1.txt" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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121 </test>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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122 <test>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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123 <param name="reference" value="Tn4401b-1.fasta" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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124 <conditional name="collection_paired">
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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125 <param name="selector" value="paired" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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126 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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127 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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128 </conditional>
1
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parents: 0
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129 <conditional name="snp_profiles_source">
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130 <param name="snp_profiles_source_selector" value="history" />
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131 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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132 </conditional>
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133 <conditional name="struct_profiles_source">
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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134 <param name="struct_profiles_source_selector" value="history" />
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135 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
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136 </conditional>
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137 <output name="summary" file="output_summary_2.txt" />
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138 </test>
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139 <test>
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parents: 0
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140 <param name="reference" value="Tn4401b-1.fasta" />
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parents: 0
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141 <conditional name="collection_paired">
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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142 <param name="selector" value="paired" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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parents: 0
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143 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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parents: 0
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144 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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145 </conditional>
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146 <conditional name="snp_profiles_source">
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147 <param name="snp_profiles_source_selector" value="tool_data_table" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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148 <param name="snp_profiles" value="Tn4401b_snp_profiles" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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149 </conditional>
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150 <conditional name="struct_profiles_source">
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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parents: 0
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151 <param name="struct_profiles_source_selector" value="tool_data_table" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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152 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
36093854bfc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
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153 </conditional>
0
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154 <output name="summary" file="output_summary_2.txt" />
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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155 </test>
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156 </tests>
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157 <help>
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158 <![CDATA[
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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159 **What it does**
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160
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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161 TETyper is designed for typing a specific transposable element (TE) of interest from paired-end sequencing data. It determines single nucleotide variants (SNVs) and deletions within the TE, as well as flanking sequences surrounding the TE.
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diff changeset
162
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
163 **Input**
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
164
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
165 **SNP Profiles**: A tab-delimited file with the following columns:
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
166
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
167 1. Profile ID
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
168 2. Homozygous SNPs
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
169 3. Heterozygous SNPs
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
170
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
171 SNPs are represented in the format [REF][POSITION][ALT], and separated by pipe (`|`) characters. SNPs should be ordered by position. Valid alt-bases for heterozygous SNPs are: `M,R,W,S,Y,K`
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
172
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
173 For example:
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
174
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
175 ::
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
176
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
177 1 none none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
178 2 C8015T none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
179 3 C8015T|T9621C none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
180 4 T7199A|C8015T|T9621C none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
181 6 C7509G|T7917G none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
182 N2 none C8015Y
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
183 N4 none A5178R
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
184 N5 none C8015Y|T9663Y
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
185
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
186 **Structural Variant Profiles**: A tab-delimited file with the following columns:
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
187
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
188 1. Profile ID
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
189 2. Structural Variants
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
190
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
191 Structural Variants are represented in the format [START-POSITION]-[END-POSITION], and separated by pipe (`|`) characters.
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
192
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
193 For example:
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
194
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
195 ::
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
196
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
197 Tn4401b none
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
198 Tn4401a 7020-7118
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
199 Tn4401h 6919-7106
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
200 Tn4401_truncC 1-7127|9198-10006
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
201
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
202 **Output**
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
203
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
204 TETyper will produce a tab-seperated output file with the following outputs:
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
205
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
206 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
207 | Column | Description |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
208 +==========================+==================================================================================================================================================================================================================================================+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
209 | Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
210 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
211 | Structural_variant | If --struct_profiles is specified and the pattern of deletions above corresponds to one of these profiles, then the profile name is given, otherwise "unknown". |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
212 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
213 | SNPs_homozygous | A list of homozygous SNPs identified, or "none". |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
214 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
215 | SNPs_heterozygous | A list of heterozygous SNPs identified, or "none". |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
216 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
217 | Heterozygous_SNP_counts | For each heterozygous SNP, the number of reads supporting the reference and alternative calls, or "none" if there are no heterozygous SNPs. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
218 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
219 | SNP_variant | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown". |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
220 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
221 | Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
222 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
223 | Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
224 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
225 | Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
226 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
227 | Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
228 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
229 | Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
230 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
231 | X_Y_presence | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. |
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
232 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
233
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
234 ]]>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
235 </help>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
236 <citations>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
237 <citation type="doi">10.1099/mgen.0.000232</citation>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
238 </citations>
8bc80c2a15b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
239 </tool>