Mercurial > repos > iuc > sniffles
annotate sniffles.xml @ 0:93c4b04a0769 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
| author | iuc |
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| date | Mon, 14 Sep 2020 07:39:07 +0000 |
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| rev | line source |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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1 <tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0"> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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2 <description>Structural variation caller using third generation sequencing</description> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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3 <macros> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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4 <token name="@TOOL_VERSION@">1.0.12</token> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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5 </macros> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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6 <requirements> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">sniffles</requirement> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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8 </requirements> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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9 <version_command> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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10 <![CDATA[ sniffles --version ]]> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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11 </version_command> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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12 <command detect_errors="exit_code"> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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13 <![CDATA[ |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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14 ln -f -s '${input}' input.bam && |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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15 ln -f -s '${input.metadata.bam_index}' input.bam.bai && |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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16 |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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17 sniffles |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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18 -t \${GALAXY_SLOTS:-2} |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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19 -m 'input.bam' |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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20 -v '$output' |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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21 ## general_options |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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22 #if $general_options.min_support: |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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23 --min_support $general_options.min_support |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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24 #end if |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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25 --max_num_splits $general_options.max_num_splits |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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26 #if $general_options.max_distance: |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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27 --max_distance $general_options.max_distance |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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28 #end if |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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29 #if $general_options.min_length: |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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30 --min_length $general_options.min_length |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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31 #end if |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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32 --minmapping_qual $general_options.minmapping_qual |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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33 --num_reads_report $general_options.num_reads_report |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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34 #if $general_options.min_seq_size: |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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35 --min_seq_size $general_options.min_seq_size |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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36 #end if |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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37 --min_zmw $general_options.min_zmw |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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38 $general_options.cs_string |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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39 ## clustering_options |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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40 $clustering_options.cluster |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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41 #if $clustering_options.cluster_support: |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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42 --cluster_support $clustering_options.cluster_support |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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43 #end if |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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44 --allelefreq $clustering_options.allelefreq |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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45 --min_homo_af $clustering_options.min_homo_af |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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46 --min_het_af $clustering_options.min_het_af |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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47 ##advanced_options |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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48 $advanced_options.report_BND |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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49 $advanced_options.not_report_seq |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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50 $advanced_options.ignore_sd |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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51 $advanced_options.ccs_reads |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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52 ## parameter_estimation_options |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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53 $parameter_estimation_options.skip_parameter_estimation |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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54 --del_ratio $parameter_estimation_options.del_ratio |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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55 --ins_ratio $parameter_estimation_options.ins_ratio |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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56 --max_diff_per_window $parameter_estimation_options.max_diff_per_window |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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57 --max_dist_aln_events $parameter_estimation_options.max_dist_aln_events |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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58 ]]> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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59 </command> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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60 <inputs> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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61 <param type="data" name="input" format="bam" label="Input BAM file"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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62 <section name="general_options" title="Set general options" expanded="False"> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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63 <param argument="--min_support" type="integer" value="10" optional="true" min="1" label="Minimum Support" help="Minimum number of reads that support a SV. [10]" /> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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64 <param argument="--max_num_splits" type="integer" value="7" optional="true" min="0" label="Maximum Number of Splits" help="Maximum number of splits per read to be still taken into account. [7]" /> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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65 <param argument="--max_distance" type="integer" value="1000" optional="true" min="10" label="Maximum Distance" help="Maximum distance to group SV together. [1000]" /> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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66 <param argument="--min_length" type="integer" value="30" optional="true" min="2" label="Minimum Length" help="Minimum length of SV to be reported. [30]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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67 <param argument="--minmapping_qual" type="integer" value="20" optional="true" min="0" label="Minimum Mapping Quality" help="Minimum Mapping Quality. [20]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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68 <param argument="--num_reads_report" type="integer" value="0" optional="true" min="-1" label="Number of reads to report" help="Report up to N reads that support the SV in the vcf file. -1: report all. [0]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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69 <param argument="--min_seq_size" type="integer" value="" optional="true" label="Minimum Seq Size" help="Discard read if non of its segment is larger then this. [2000]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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70 <param argument="--min_zmw" type="integer" value="0" optional="true" min="0" label="Minimum ZMW" help="Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. [0]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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71 <param argument="--cs_string" type="boolean" truevalue="--cs_string" falsevalue="" optional="true" label="Enable CS String" help="Enables the scan of CS string instead of Cigar and MD. [false]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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72 </section> |
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93c4b04a0769
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73 <section name="clustering_options" title="Clustering/phasing and genotyping options" expanded="False"> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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74 <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" optional="true" label="Cluster" help="Enables Sniffles to phase SVs that occur on the same reads [false]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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75 <param argument="--cluster_support" type="integer" value="1" optional="true" min="1" label="Cluster Support" help="Minimum number of reads supporting clustering of SV. [1]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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76 <param argument="--allelefreq" type="float" value="0" optional="true" min="0" label="Allele Frequency Threshold" help="Filters the SV calls based on the allele frequency. [0]" /> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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77 <param argument="--min_homo_af" type="float" value="0.8" optional="true" min="0" max="1" label="Minimum Homogenous Allele Frequency" help="Minimum homogeneous threshold on allele frequency (0-1). [0.8]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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78 <param argument="--min_het_af" type="float" value="0.3" optional="true" min="0" max="1" label="Minimum Heterogeneous Allele Frequency" help="Minimum heterogeneous threshold on allele frequency (0-1). [0.3]"/> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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79 </section> |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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80 <section name="advanced_options" title="Advanced options" expanded="False"> |
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81 <param argument="--report_BND" type="boolean" value="True" truevalue="--report_BND" falsevalue="" optional="true" label="Report BND" help="Report BND instead of Tra in vcf output. [true]" /> |
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82 <param argument="--not_report_seq" type="boolean" value="False" truevalue="--not_report_seq" falsevalue="" optional="true" label="Don't report seq" help="Don't report sequences for indels in vcf output. (Beta version!) [false]"/> |
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83 <param argument="--ignore_sd" type="boolean" value="False" truevalue="--ignore_sd" falsevalue="" optional="true" label="Igonore sd" help="Ignores the sd based filtering. [false]"/> |
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84 <param argument="--ccs_reads" type="boolean" value="False" truevalue="--ccs_reads" falsevalue="" optional="true" label="CCS Reads" help="Preset CCS Pacbio setting. (Beta) [false]" /> |
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85 </section> |
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86 <section name="parameter_estimation_options" title="Parameter Estimation Options" expanded="False"> |
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87 <param argument="--skip_parameter_estimation" type="boolean" value="False" truevalue="--skip_parameter_estimation" falsevalue="" optional="true" label="Skip Parameter Estimation" help="Enables the scan if only very few reads are present. [false]"/> |
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88 <param argument="--del_ratio" type="float" value="0.0458369" optional="true" min="0" max="1" label="Estimated Deletion Ratio" help="Estimated ratio of deletions per read (0-1). [0.0458369]" /> |
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89 <param argument="--ins_ratio" type="float" value="0.049379" optional="true" min="0" max="1" label="Estimated Insertion Ratio" help="Estimated ratio of insertions per read (0-1). [0.049379]" /> |
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90 <param argument="--max_diff_per_window" type="integer" value="50" optional="true" min="0" label="Maximum Differences Per Window" help="Maximum differences per 100bp. [50]"/> |
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91 <param argument="--max_dist_aln_events" type="integer" value="4" optional="true" min="0" label="Maximum Distance Between Alignment Events" help="Maximum distance between alignment (indel) events. [4]"/> |
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92 </section> |
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93 </inputs> |
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94 <outputs> |
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95 <data name="output" format="vcf" label="${tool.name} on ${on_string}"/> |
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96 </outputs> |
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97 <tests> |
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98 <test> <!-- test 1 - standard run --> |
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99 <param name="input" value="reads_region.bam"/> |
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100 <param name="output_format" value="vcf"/> |
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101 <output name="output" file="expected_output.vcf" lines_diff="2"/> |
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102 </test> |
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103 <test> <!-- test 2 - add reads into report --> |
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104 <param name="input" value="reads_region.bam"/> |
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105 <param name="output_format" value="vcf"/> |
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106 <param name="num_reads_report" value="-1"/> |
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107 <output name="output" file="expected_output2.vcf" lines_diff="2"/> |
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108 </test> |
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109 <test> <!-- test 3 - use cs_string --> |
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110 <param name="input" value="reads_region.bam"/> |
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111 <param name="output_format" value="vcf"/> |
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112 <param name="cs_string" value="true"/> |
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113 <output name="output" file="expected_outcome3.vcf" lines_diff="2"/> |
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114 </test> |
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115 <test> <!-- test 4 - clustering --> |
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116 <param name="input" value="reads_region.bam"/> |
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117 <param name="output_format" value="vcf"/> |
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118 <param name="cluster" value="True"/> |
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119 <output name="output" file="expected_outcome4.vcf" lines_diff="2"/> |
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120 </test> |
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121 <test> <!-- test 5 - Advanced - Report BND --> |
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122 <param name="input" value="reads_region.bam"/> |
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123 <param name="output_format" value="vcf"/> |
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124 <param name="report_BND" value="True"/> |
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125 <output name="output" file="expected_outcome5.vcf" lines_diff="2"/> |
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126 </test> |
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127 <test> <!-- test 6 - Parameter Estimation - skip --> |
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128 <param name="input" value="reads_region.bam"/> |
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129 <param name="output_format" value="vcf"/> |
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130 <param name="skip_parameter_estimation" value="True"/> |
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131 <output name="output" file="expected_outcome6.vcf" lines_diff="2"/> |
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132 </test> |
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133 </tests> |
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134 <help> |
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135 <![CDATA[ |
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136 ######## |
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137 Sniffles |
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138 ######## |
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139 |
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140 What is Sniffles? |
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141 ***************** |
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142 Sniffles is a SV caller for long reads. It is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). Furthermore, Sniffles incorporates multiple auto tuning functions to determine data set depending parameter to reduce the overall risk of falsely infer SVs. |
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143 |
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144 Quick Start |
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145 *********** |
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146 |
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147 Make sure you have a sorted bam file either from ngmlr or from bwa. For the later make sure you have used -M parameter for mapping to mark which alignments are primary and which are secondary! Note you have to adjust the parameters for low coverage cases. |
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148 |
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149 Parameters |
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150 ********** |
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151 |
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152 General |
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153 ------- |
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154 |
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155 +---------------------------+-----------------------------------------------------------------------+ |
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156 | Parameter | Description | |
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157 +===========================+=======================================================================+ |
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158 | Minimum Support | Minimum number of reads that support a SV to be reported. Default: 10 | |
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159 +---------------------------+-----------------------------------------------------------------------+ |
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160 | Maximum Number of Splits | Maximum number of split segments a read is aligned at before it is | |
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161 | | ignored. Default: 7 | |
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162 +---------------------------+-----------------------------------------------------------------------+ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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163 | Maximum Distance | Maximum distance to group SV together. Sniffles estimates this | |
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164 | | parameter during runtime to group together SVs reported by different | |
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165 | | reads. Default: 1kb | |
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166 +---------------------------+-----------------------------------------------------------------------+ |
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167 | Minimum Length | Minimum length of SV to be reported. Default: 30bp | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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168 +---------------------------+-----------------------------------------------------------------------+ |
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169 | Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | |
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170 | | Default: 20 | |
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171 +---------------------------+-----------------------------------------------------------------------+ |
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172 | Number of Reads to Report | Number of read names to be reported that support the SV in the vcf | |
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173 | | file. Default: 0 | |
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174 +---------------------------+-----------------------------------------------------------------------+ |
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175 | Minimum Seq Size | Discard read if none of its segment is larger then this. Default: 2kb | |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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176 +---------------------------+-----------------------------------------------------------------------+ |
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177 | Minimum ZMW | Discard SV that are not supported by at least x zmws. This applies | |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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178 | | only for PacBio recognizable reads. Default: 0 | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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179 +---------------------------+-----------------------------------------------------------------------+ |
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180 | Enable CS String | Enables the scan of CS string instead of Cigar and MD. Default: False| |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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181 +---------------------------+-----------------------------------------------------------------------+ |
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182 |
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183 | |
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184 |
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185 Clustering Options |
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186 ------------------ |
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187 |
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188 +----------------------------------------+-----------------------------------------------------------------------+ |
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189 | Parameter | Description | |
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190 +========================================+=======================================================================+ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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191 | Cluster | Performs read based phasing to mark SVs that occur together. | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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192 +----------------------------------------+-----------------------------------------------------------------------+ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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193 | Cluster Support | Minimum number of reads supporting clustering of SV. Default: 1 | |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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194 +----------------------------------------+-----------------------------------------------------------------------+ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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195 | Allele Frequency Threshold | Filters the SV calls based on the allele frequency. Default: 0.0 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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196 +----------------------------------------+-----------------------------------------------------------------------+ |
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197 | Minimum Homogenous Allele Frequency | Minimum homogeneous threshold on allele frequency. Default: 0.8 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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198 +----------------------------------------+-----------------------------------------------------------------------+ |
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199 | Minimum Heterogeneous Allele Frequency | Minimum heterogeneous threshold on allele frequency. Default: 0.3 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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200 +----------------------------------------+-----------------------------------------------------------------------+ |
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201 |
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202 | |
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203 |
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204 Advanced Options |
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205 ---------------- |
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206 |
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207 +----------------------------------------+------------------------------------------------------------------------+ |
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93c4b04a0769
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208 | Parameter | Description | |
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209 +========================================+========================================================================+ |
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210 | Report BND | Reports the inversions and translocations as BND events. Default: False| |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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211 +----------------------------------------+------------------------------------------------------------------------+ |
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212 | Don't Report Seq | Don't report sequences for indels in vcf output. (Beta version!) | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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213 | | Default: False | |
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214 +----------------------------------------+------------------------------------------------------------------------+ |
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215 | Ignore sd | Ignores the sd based filtering. Default: False | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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216 +----------------------------------------+------------------------------------------------------------------------+ |
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217 | CCS Reads | Preset CCS Pacbio setting. (Beta) Default: False | |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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218 +----------------------------------------+------------------------------------------------------------------------+ |
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219 |
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220 | |
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221 |
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222 Parameter Estimation Options |
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223 ---------------------------- |
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224 |
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225 +----------------------------------------+------------------------------------------------------------------------+ |
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226 | Parameter | Description | |
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227 +========================================+========================================================================+ |
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228 | Skip Parameter Estimation | Enables the scan if only very few reads are present. Default: False | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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229 +----------------------------------------+------------------------------------------------------------------------+ |
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230 | Estimated Deletion Ratio | Estimated ratio of deletions per read. Default: 0.0458369 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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231 +----------------------------------------+------------------------------------------------------------------------+ |
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iuc
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232 | Estimated Insertion Ratio | Estimated ratio of insertions per read. Default: 0.049379 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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233 +----------------------------------------+------------------------------------------------------------------------+ |
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234 | Maximum Differences Per Window | Maximum differences per 100bp. Default: 50 | |
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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235 +----------------------------------------+------------------------------------------------------------------------+ |
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iuc
parents:
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236 | Maximum Distance Between Alignment | Maximum distance between alignment (indel) events. Default: 4 | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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237 | Events | | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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238 +----------------------------------------+------------------------------------------------------------------------+ |
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239 |
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240 | |
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241 |
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242 Output |
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243 ****** |
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244 |
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245 VCF Info field description |
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246 | |
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247 Sniffles report multiple information in the Info field. The entries are delimited by: |
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248 | |
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249 +-------------------+------------------------------------------------------------------------------------------------------+ |
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250 | IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). | |
|
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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251 +-------------------+------------------------------------------------------------------------------------------------------+ |
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252 | CHR2= | The chromosome of the second breakpoint of the SV reported. | |
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253 +-------------------+------------------------------------------------------------------------------------------------------+ |
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254 | END= | The position (bp) of the second breakpoint of the SV reported. | |
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255 +-------------------+------------------------------------------------------------------------------------------------------+ |
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256 | ZMW= | For PacBio based reads, shows the number of ZMW that support the SV. | |
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257 +-------------------+------------------------------------------------------------------------------------------------------+ |
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258 | SVTYPE= | The type of the SV. (see Alt field above) | |
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259 +-------------------+------------------------------------------------------------------------------------------------------+ |
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260 | SUPTYPE= | Indicates what evidence supports the SVs (SR: Split Reads, AL: Alignment, NR: Noisy Region). | |
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261 +-------------------+------------------------------------------------------------------------------------------------------+ |
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262 | STD_quant_start= | The standard deviation of the start breakpoints. | |
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263 +-------------------+------------------------------------------------------------------------------------------------------+ |
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264 | STD_quant_stop= | The standard deviation of the stop breakpoints. | |
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265 +-------------------+------------------------------------------------------------------------------------------------------+ |
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266 | RNAMES= | A comma separated list of read names that support the SV event. Controlled by -n Parameter. | |
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267 +-------------------+------------------------------------------------------------------------------------------------------+ |
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268 | SVLEN= | Indicates the length of SVs. | |
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269 +-------------------+------------------------------------------------------------------------------------------------------+ |
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270 | STRANDS= | Strand information at both breakpoints. | |
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271 +-------------------+------------------------------------------------------------------------------------------------------+ |
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272 | SEQ= | If reportable shows the sequence of the indels. | |
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273 +-------------------+------------------------------------------------------------------------------------------------------+ |
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274 | RE= | Number of reads supporting the variance. | |
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275 +-------------------+------------------------------------------------------------------------------------------------------+ |
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276 | AF= | Allele frequency (only if run with –genotype) | |
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277 +-------------------+------------------------------------------------------------------------------------------------------+ |
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278 | |
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279 Source: https://github.com/fritzsedlazeck/Sniffles/wiki |
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280 ]]> |
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281 </help> |
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282 <citations> |
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283 <citation type="doi">10.1038/s41592-018-0001-7</citation> |
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284 </citations> |
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285 </tool> |