Mercurial > repos > iuc > ivar_trim

annotate ivar_trim.xml @ 12:806372ff89b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
author iuc
date Wed, 11 Jan 2023 09:51:30 +0000
parents a523c1c3ac32
children a15b0f953cf8
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12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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1 <tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
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2 <description>Trim reads in aligned BAM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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6 <expand macro="requirements"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $primer.source == 'history'
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10 cp '$primer.input_bed' bed.bed &&
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11 #else
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12 cp '$primer.cached_bed.fields.path' bed.bed &&
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13 #end if
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14 python '$__tool_directory__/sanitize_bed.py' bed.bed &&
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15 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
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16 #if $amplicons.filter_by == 'yes_compute':
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17 python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv &&
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18 #else
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19 ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv &&
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20 #end if
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21 python '$__tool_directory__/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv &&
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22 #end if
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23 ln -s '$input_bam' sorted.bam &&
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24 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
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25
0
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26 ivar trim
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27 -i sorted.bam
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28 -b bed.bed
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29 #if $amplicons.filter_by == 'yes'
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30 -f amplicon_info.tsv
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31 #end if
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32 -x $primer_pos_wiggle
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33 $inc_primers
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34 -m $min_len
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35 -q $min_qual
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36 -s $window_width
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37 -p trimmed &&
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38 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam
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39 ]]> </command>
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40 <inputs>
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41 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
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42 <conditional name="primer">
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43 <param label="Source of primer information" name="source" type="select">
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44 <option value="history" selected="true">History</option>
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45 <option value="cached">Built-in</option>
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46 </param>
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47 <when value="history">
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48 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
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49 </when>
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50 <when value="cached">
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51 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
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52 <options from_data_table="primer_scheme_bedfiles">
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53 <filter type="sort_by" column="1" />
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54 <validator type="no_options" message="No primer schemes are available" />
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55 </options>
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56 </param>
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57 </when>
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58 </conditional>
5
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59 <conditional name="amplicons">
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60 <param name="filter_by" type="select"
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61 label="Filter reads based on amplicon info"
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62 help="When you select Yes, reads that are not fully contained in any amplicon will be dropped before primer trimming. This option is currently marked as [Experimental] in ivar, but nevertheless recommended here. Info on amplicons can be computed from suitable primer BED files (see tool help below) or provided by the user. ">
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63 <option value="">No, allow reads to extend beyond amplicon boundaries</option>
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64 <option value="yes_compute">Yes, drop reads that extend beyond amplicon boundaries</option>
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65 <option value="yes">Yes, drop reads that extend beyond amplicon boundaries and use my amplicon info file</option>
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66 </param>
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67 <when value="yes_compute" />
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68 <when value="yes">
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69 <param name="amplicon_info" argument="-f" type="data" format="tabular" />
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70 </when>
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71 <when value="" />
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72 </conditional>
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73 <param name="primer_pos_wiggle" argument="-x" type="integer" min="0" value="0"
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74 label="Wiggling room for read ends relative to primer binding sites"
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75 help="Reads that occur at the specified offset positions relative to primer positions (as annotated in the primer information dataset) will also be trimmed (default: 0)" />
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76 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/>
0
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77 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
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78 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
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79 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
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80 </inputs>
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81 <outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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82 <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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diff changeset
83 </outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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diff changeset
84 <tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
85 <!-- #1: SARS-Cov data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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diff changeset
86 <test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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diff changeset
87 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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diff changeset
88 <param name="input_bed" value="covid19/ARTIC-V1.bed" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
89 <param name="inc_primers" value="true" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
90 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
91 </test>
4
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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diff changeset
92 <test>
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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diff changeset
93 <!-- Test with primer bed file that needs to be sanitized -->
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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diff changeset
94 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents: 3
diff changeset
95 <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" />
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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diff changeset
96 <param name="inc_primers" value="true" />
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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diff changeset
97 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
3c20a5cc3914 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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parents: 3
diff changeset
98 </test>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
99 <!-- #1: Zika data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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100 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
101 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
102 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
103 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
104 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
105 <param name="input_bam" value="zika/Z52_a.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
106 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
107 </test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
108 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
109 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
110 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
111 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
112 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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diff changeset
113 <param name="input_bam" value="zika/Z52_b.sorted.bam" />
12
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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parents: 11
diff changeset
114 <output name="output_bam" ftype="bam">
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115 <assert_contents>
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diff changeset
116 <has_size value="4023965" delta="1000"/>
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diff changeset
117 </assert_contents>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
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diff changeset
118 </output>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
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diff changeset
119 <assert_stdout>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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diff changeset
120 <has_text text="Found 68 primers in BED file"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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diff changeset
121 <has_text text="Using Region: PRV"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
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diff changeset
122 <has_text text="Found 40964 mapped reads"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
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diff changeset
123 <has_text text="reads were quality trimmed below the minimum length of 30 bp and were not written to file"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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diff changeset
124 <has_text text="reads that started outside of primer regions were not written to file"/>
806372ff89b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
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125 </assert_stdout>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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126 </test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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127 <test>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
128 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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diff changeset
129 <param name="source" value="cached" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
130 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
131 </conditional>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
132 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
133 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
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parents: 0
diff changeset
134 </test>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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parents: 5
diff changeset
135 <test>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
136 <conditional name="primer">
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents: 5
diff changeset
137 <param name="source" value="cached" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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diff changeset
138 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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139 </conditional>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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140 <conditional name="amplicons">
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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diff changeset
141 <param name="filter_by" value="yes_compute" />
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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142 </conditional>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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parents: 5
diff changeset
143 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
10
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
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144 <assert_command>
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
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145 <has_text text="write_amplicon_info_file" />
b716d7eba443 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"
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146 </assert_command>
8
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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147 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/>
509652d89290 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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diff changeset
148 </test>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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149 </tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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150 <help><![CDATA[
5
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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151 iVar uses primer positions supplied in a BED file to soft clip primer
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diff changeset
152 sequences from an aligned and sorted BAM file. Following this, the reads are
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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153 trimmed further based on a quality threshold.
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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parents: 4
diff changeset
154
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
155 **Primer and Amplicon info**
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
156
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
157 The tool requires information about primers and their binding sites in 6-column
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
158 BED format. The information from this file is used to decide whether any mapped
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diff changeset
159 read in the BAM input ends with a primer sequence and should, thus, be
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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parents: 4
diff changeset
160 soft-clipped.
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parents: 4
diff changeset
161
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
162 Optionally, the tool can also discard reads that do not fully map to within any
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
163 amplicon. Such reads are likely to be wet-lab or mapping artefacts and removing
6c80028c6d83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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diff changeset
164 them can increase variant calling precision. To calculate the extent of
9
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165 expected amplicons the tool needs to know which primers work together to form
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166 an amplicon. The tool can try to deduce this info from the names of the primers
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167 found in the primer info dataset. This will require a primer naming scheme
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168 following the regex pattern::
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169
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170 .*_(?P<amplicon_number>\d+).*_(?P<primer_orientation>L(?:EFT)?|R(?:IGHT)?)
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171
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172 *i.e.*, the following schemes will work (and get parsed as):
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173
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174 - ``nCoV-2019_1_LEFT`` (forward primer of amplicon 1)
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175
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176 - ``400_2_out_R`` (reverse primer of amplicon 2)
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177
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178 - ``QIAseq_163-2_LEFT`` (forward primer of amplicon 163)
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179
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180 Alternatively, you can specify the amplicon information explicitly through a
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181 dataset that lists the names of primers that together form any given amplicon.
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182 In it, primer names (exactly matching those in the primer info dataset) need to
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183 be TAB-separated with one line per amplicon.
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184 If the primer scheme has more than two primers contributing to a given amplicon
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185 (in schemes using alternate primers), you can (in this Galaxy tool only)
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186 specify all of them on one line and the tool will calculate the maximum extent
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187 of the amplicon.
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188
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189 **Quality trimming details**
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190
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191 To do the quality trimming, iVar uses a sliding window approach. The window
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192 slides from the 5' end to the 3' end and if at any point the average base
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193 quality in the window falls below the threshold, the remaining read is soft
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194 clipped. If after trimming, the length of the read is greater than the minimum
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195 length specified, the read is written to the new trimmed BAM file.
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196
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197 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
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198 ]]></help>
0
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199 <expand macro="citations" />
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200 </tool>