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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
author iuc
date Sun, 15 Dec 2024 09:07:56 +0000
parents 287335d65198
children
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2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
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1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy2" profile="23.1">
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2 <description>Transposable Element Typer</description>
becaebddb198 "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>
becaebddb198 "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>
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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
287335d65198 "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
becaebddb198 "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}
becaebddb198 "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}'
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17 #elif $collection_paired.selector == "collection":
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18 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
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19 #end if
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20 --ref 'reference.fa'
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21 --flank_len '${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'
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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'
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30 #end if
1
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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'
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35 #end if
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36 --outprefix output
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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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83 label="Structural Variant Profile">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
84 <options from_data_table="tetyper_struct_profiles">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
85 <validator type="no_options" message="No TETyper structural variant profiles are available" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
86 </options>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
87 </param>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
88 </when>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
89 <when value="history">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
90 <param name="struct_profiles" type="data" format="tabular"
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
91 label="Structural Variant Profile"
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
92 help="A two-column tabular file with structural variant profile definitions"/>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
93 </when>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
94 </conditional>
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
95 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
96 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
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."/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
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."/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
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."/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
100 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
101 <param name="include_log" type="boolean" label="Include log in output"/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
102 </inputs>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
103 <outputs>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
104 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
105 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
106 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
107 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/>
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
108 <data name="log" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
109 <filter>include_log</filter>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
110 </data>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
111 </outputs>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
112 <tests>
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
113 <test expect_num_outputs="4">
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
114 <param name="reference" value="Tn4401b-1.fasta" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
115 <conditional name="collection_paired">
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
116 <param name="selector" value="paired" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
117 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
118 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
119 </conditional>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
120 <output name="summary" file="output_summary_1.txt" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
121 </test>
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
122 <test expect_num_outputs="4">
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
123 <param name="reference" value="Tn4401b-1.fasta" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
124 <conditional name="collection_paired">
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
125 <param name="selector" value="paired" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
126 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
127 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
128 </conditional>
1
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
129 <conditional name="snp_profiles_source">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
130 <param name="snp_profiles_source_selector" value="history" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
131 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
132 </conditional>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
133 <conditional name="struct_profiles_source">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
134 <param name="struct_profiles_source_selector" value="history" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
135 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
136 </conditional>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
137 <output name="summary" file="output_summary_2.txt" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
138 </test>
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
139 <test expect_num_outputs="5">
1
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
140 <param name="reference" value="Tn4401b-1.fasta" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
141 <conditional name="collection_paired">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
142 <param name="selector" value="paired" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
143 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
144 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
145 </conditional>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
146 <conditional name="snp_profiles_source">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
147 <param name="snp_profiles_source_selector" value="tool_data_table" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
148 <param name="snp_profiles" value="Tn4401b_snp_profiles" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
149 </conditional>
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
150 <conditional name="struct_profiles_source">
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
151 <param name="struct_profiles_source_selector" value="tool_data_table" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
152 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
ea4310309d66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents: 0
diff changeset
153 </conditional>
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
154 <param name="include_log" value="true"/>
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
155 <output name="summary" file="output_summary_2.txt" />
3
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
156 <output name="snps">
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
157 <assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
158 <has_size min="1"/>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
159 </assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
160 </output>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
161 <output name="blast">
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
162 <assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
163 <has_n_lines n="2"/>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
164 <has_n_columns n="12"/>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
165 </assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
166 </output>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
167 <output name="alignment">
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
168 <assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
169 <has_size min="1"/>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
170 </assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
171 </output>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
172 <output name="log">
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
173 <assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
174 <has_text text="Final output written to: output_summary.txt"/>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
175 </assert_contents>
2ccf19849796 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
iuc
parents: 2
diff changeset
176 </output>
0
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
177 </test>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
178 </tests>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
179 <help>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
180 <![CDATA[
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
181 **What it does**
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
182
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
183 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.
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
184
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
185 **Input**
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
186
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
187 **SNP Profiles**: A tab-delimited file with the following columns:
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
188
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
189 1. Profile ID
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
190 2. Homozygous SNPs
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
191 3. Heterozygous SNPs
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
192
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
193 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`
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
194
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
195 For example:
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
196
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
197 ::
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
198
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
199 1 none none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
200 2 C8015T none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
201 3 C8015T|T9621C none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
202 4 T7199A|C8015T|T9621C none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
203 6 C7509G|T7917G none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
204 N2 none C8015Y
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
205 N4 none A5178R
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
206 N5 none C8015Y|T9663Y
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
207
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
208 **Structural Variant Profiles**: A tab-delimited file with the following columns:
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
209
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
210 1. Profile ID
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
211 2. Structural Variants
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
212
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
213 Structural Variants are represented in the format [START-POSITION]-[END-POSITION], and separated by pipe (`|`) characters.
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
214
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
215 For example:
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
216
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
217 ::
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
218
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
219 Tn4401b none
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
220 Tn4401a 7020-7118
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
221 Tn4401h 6919-7106
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
222 Tn4401_truncC 1-7127|9198-10006
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
223
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
224 **Output**
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
225
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
226 TETyper will produce a tab-seperated output file with the following outputs:
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
227
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
228 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
229 | Column | Description |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
230 +==========================+==================================================================================================================================================================================================================================================+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
231 | Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
232 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
233 | 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". |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
234 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
235 | SNPs_homozygous | A list of homozygous SNPs identified, or "none". |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
236 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
237 | SNPs_heterozygous | A list of heterozygous SNPs identified, or "none". |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
238 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
239 | 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. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
240 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
241 | 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". |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
242 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
243 | Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
244 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
245 | Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
246 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
247 | Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
248 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
249 | Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
250 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
251 | Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
252 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff changeset
253 | 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. |
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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254 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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255
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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256 ]]>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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257 </help>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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258 <citations>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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259 <citation type="doi">10.1099/mgen.0.000232</citation>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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260 </citations>
becaebddb198 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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261 </tool>