Mercurial > repos > iuc > tetyper
annotate tetyper.xml @ 1:36093854bfc7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
author | iuc |
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date | Sat, 18 Jan 2020 15:04:39 -0500 |
parents | 8bc80c2a15b3 |
children | edcf603bedfd |
rev | line source |
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1
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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changeset
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1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1"> |
0
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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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"
iuc
parents:
diff
changeset
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3 <macros> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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4 <token name="@TOOL_VERSION@">1.1</token> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
5 </macros> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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6 <requirements> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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7 <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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8 </requirements> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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9 <command detect_errors="exit_code"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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10 <![CDATA[ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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11 TETyper.py |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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12 --threads \${GALAXY_SLOTS:-1} |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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13 #if $collection_paired.selector == "paired" |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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14 --fq1 '${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"
iuc
parents:
diff
changeset
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15 #elif $collection_paired.selector == "collection": |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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16 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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17 #end if |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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18 --ref '${reference}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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19 --flank_len '${flank_length}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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20 --min_reads '${min_reads}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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21 --min_each_strand '${min_each_strand}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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22 --min_mapped_len '${min_mapped_len}' |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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23 --min_qual '${min_qual}' |
1
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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24 #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table": |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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changeset
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25 --snp_profiles '$snp_profiles_source.snp_profiles.fields.path' |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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26 #elif str( $snp_profiles_source.snp_profiles_source_selector ) == 'history': |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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27 --snp_profiles '$snp_profiles_source.snp_profiles' |
0
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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28 #end if |
1
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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29 #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table": |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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30 --struct_profiles '$struct_profiles_source.struct_profiles.fields.path' |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
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31 #elif str( $struct_profiles_source.struct_profiles_source_selector ) == 'history': |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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32 --struct_profiles '$struct_profiles_source.struct_profiles' |
0
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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33 #end if |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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34 --outprefix output |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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35 ]]> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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changeset
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36 </command> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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37 <inputs> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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38 <conditional name="collection_paired"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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39 <param name="selector" type="select" label="Collection or paired reads" > |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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40 <option value="collection">Collection</option> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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41 <option value="paired" selected="True">Paired</option> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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42 </param> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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43 <when value="collection"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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44 <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" /> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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45 </when> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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46 <when value="paired"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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47 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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48 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
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49 </when> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
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50 </conditional> |
1
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
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51 <conditional name="snp_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
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52 <param name="snp_profiles_source_selector" type="select" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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53 label="Select a SNP profile from your history or use one from a tool data table?"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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54 <option value="No" selected="true">No SNP profile</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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55 <option value="tool_data_table">SNP profile from tool data table</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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56 <option value="history">SNP profile from history</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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57 </param> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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58 <when value="No"/> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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59 <when value="tool_data_table"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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60 <param name="snp_profiles" type="select" format="tabular" label="SNP Profile"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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61 <options from_data_table="tetyper_snp_profiles"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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62 <validator type="no_options" message="No TETyper SNP profiles are available" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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63 </options> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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64 </param> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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65 </when> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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66 <when value="history"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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67 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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68 help="A three-column tabular file with SNP profile definitions"/> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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69 </when> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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70 </conditional> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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71 <conditional name="struct_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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72 <param name="struct_profiles_source_selector" type="select" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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73 label="Select a structural variant profile from your history or use one from a tool data table?"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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74 <option value="No" selected="true">No structural variant profile</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
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|
75 <option value="tool_data_table">Structural variant profile from tool data table</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
76 <option value="history" selected="true">Structural variant profile from history</option> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
77 </param> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
78 <when value="No"/> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
79 <when value="tool_data_table"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
80 <param name="struct_profiles" type="select" format="tabular" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
81 label="Structural Variant Profile"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
82 <options from_data_table="tetyper_struct_profiles"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
83 <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"
iuc
parents:
0
diff
changeset
|
84 </options> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
85 </param> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
86 </when> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
87 <when value="history"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
88 <param name="struct_profiles" type="data" format="tabular" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
89 label="Structural Variant Profile" |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
90 help="A two-column tabular file with structural variant profile definitions"/> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
91 </when> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
92 </conditional> |
0
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
93 <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"
iuc
parents:
diff
changeset
|
94 <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"
iuc
parents:
diff
changeset
|
95 <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"
iuc
parents:
diff
changeset
|
96 <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"
iuc
parents:
diff
changeset
|
97 <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"
iuc
parents:
diff
changeset
|
98 <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"
iuc
parents:
diff
changeset
|
99 <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"
iuc
parents:
diff
changeset
|
100 </inputs> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
101 <outputs> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
102 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
103 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
104 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
105 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
106 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
107 <filter>include_log</filter> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
108 </data> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
109 </outputs> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
110 <tests> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
111 <test> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
112 <param name="reference" value="Tn4401b-1.fasta" /> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
113 <conditional name="collection_paired"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
114 <param name="selector" value="paired" /> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
115 <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"
iuc
parents:
diff
changeset
|
116 <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"
iuc
parents:
diff
changeset
|
117 </conditional> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
118 <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"
iuc
parents:
diff
changeset
|
119 </test> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
120 <test> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
121 <param name="reference" value="Tn4401b-1.fasta" /> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
122 <conditional name="collection_paired"> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
123 <param name="selector" value="paired" /> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
changeset
|
124 <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"
iuc
parents:
diff
changeset
|
125 <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"
iuc
parents:
diff
changeset
|
126 </conditional> |
1
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
127 <conditional name="snp_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
128 <param name="snp_profiles_source_selector" value="history" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
129 <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"
iuc
parents:
0
diff
changeset
|
130 </conditional> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
131 <conditional name="struct_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
132 <param name="struct_profiles_source_selector" value="history" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
133 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
134 </conditional> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
135 <output name="summary" file="output_summary_2.txt" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
136 </test> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
137 <test> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
138 <param name="reference" value="Tn4401b-1.fasta" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
139 <conditional name="collection_paired"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
140 <param name="selector" value="paired" /> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
141 <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"
iuc
parents:
0
diff
changeset
|
142 <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"
iuc
parents:
0
diff
changeset
|
143 </conditional> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
144 <conditional name="snp_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
145 <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"
iuc
parents:
0
diff
changeset
|
146 <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"
iuc
parents:
0
diff
changeset
|
147 </conditional> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
148 <conditional name="struct_profiles_source"> |
36093854bfc7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
iuc
parents:
0
diff
changeset
|
149 <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"
iuc
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150 <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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151 </conditional> |
0
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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152 <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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153 </test> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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154 </tests> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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155 <help> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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156 <![CDATA[ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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157 **What it does** |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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158 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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159 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. |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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160 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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161 **Input** |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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162 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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163 **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
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164 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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165 1. Profile ID |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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166 2. Homozygous SNPs |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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167 3. Heterozygous SNPs |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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168 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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169 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
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170 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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171 For example: |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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172 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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173 :: |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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174 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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175 1 none none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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176 2 C8015T none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
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|
177 3 C8015T|T9621C none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
178 4 T7199A|C8015T|T9621C none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
179 6 C7509G|T7917G none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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180 N2 none C8015Y |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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181 N4 none A5178R |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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182 N5 none C8015Y|T9663Y |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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183 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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184 **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
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185 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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186 1. Profile ID |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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187 2. Structural Variants |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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188 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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189 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
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190 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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191 For example: |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
192 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
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|
193 :: |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
194 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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195 Tn4401b none |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
diff
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|
196 Tn4401a 7020-7118 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
197 Tn4401h 6919-7106 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
198 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:
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199 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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200 **Output** |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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201 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
202 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
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203 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
204 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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205 | Column | Description | |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
206 +==========================+==================================================================================================================================================================================================================================================+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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207 | 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:
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208 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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209 | 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:
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210 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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211 | 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:
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212 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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213 | 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:
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214 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
215 | 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:
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|
216 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
217 | 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:
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218 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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219 | 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:
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220 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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|
221 | 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:
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222 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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223 | 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:
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|
224 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
parents:
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225 | 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:
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|
226 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
iuc
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227 | 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"
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228 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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229 | 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"
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230 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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231 |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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232 ]]> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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233 </help> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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234 <citations> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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235 <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"
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236 </citations> |
8bc80c2a15b3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"
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237 </tool> |