Mercurial > repos > iuc > ivar_trim
annotate ivar_trim.xml @ 8:397e5f0eb3ef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
author | iuc |
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date | Thu, 05 Aug 2021 12:46:37 +0000 |
parents | cf65217ad61c |
children | c092052ed673 |
rev | line source |
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8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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1 <tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy1"> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
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2 <description>Trim reads in aligned BAM</description> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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3 <macros> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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4 <import>macros.xml</import> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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5 </macros> |
4
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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6 <expand macro="requirements"> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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7 <requirement type="package" version="3.8.1">python</requirement> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
3
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8 </expand> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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9 <expand macro="version_command" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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11 #if $primer.source == 'history' |
4
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
3
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12 cp '$primer.input_bed' bed.bed && |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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13 #else |
4
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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14 cp '$primer.cached_bed.fields.path' bed.bed && |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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15 #end if |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
3
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16 python '$__tool_directory__/sanitize_bed.py' bed.bed && |
8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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17 #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_computed' |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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18 #if $amplicons.filter_by == 'yes_computed': |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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19 python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv && |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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20 #else |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
5
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21 ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv && |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
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22 #end if |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
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23 python '$__tool_directory__/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv && |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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24 #end if |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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25 ln -s '$input_bam' sorted.bam && |
4
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
3
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26 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
3
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27 |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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28 ivar trim |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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29 -i sorted.bam |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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30 -b bed.bed |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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31 #if $amplicons.filter_by == 'yes' |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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32 -f amplicon_info.tsv |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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33 #end if |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
4
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34 -x $primer_pos_wiggle |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
4
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35 $inc_primers |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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36 -m $min_len |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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37 -q $min_qual |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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38 -s $window_width |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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39 -p trimmed && |
3
5d6ed46cc101
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"
iuc
parents:
2
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40 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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41 ]]> </command> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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42 <inputs> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
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43 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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44 <conditional name="primer"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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45 <param label="Source of primer information" name="source" type="select"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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46 <option value="history" selected="true">History</option> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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47 <option value="cached">Built-in</option> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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48 </param> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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49 <when value="history"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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50 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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51 </when> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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52 <when value="cached"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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53 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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54 <options from_data_table="primer_scheme_bedfiles"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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55 <filter type="sort_by" column="1" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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56 <validator type="no_options" message="No primer schemes are available" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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57 </options> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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58 </param> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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59 </when> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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60 </conditional> |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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61 <conditional name="amplicons"> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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62 <param name="filter_by" type="select" |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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63 label="Filter reads based on amplicon info" |
8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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64 help="When you select Yes reads that are not fully contained in any amplicon will be dropped before primer trimming. Info on amplicons can be computed from the primer BED file or provided by the user. This option is currently marked as [Experimental] in ivar, but nevertheless recommended here."> |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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65 <option value="">No, allow reads to extend beyond amplicon boundaries</option> |
8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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66 <option value="yes_compute">Yes, drop reads that extend beyond amplicon boundaries</option> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
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67 <option value="yes">Yes, drop reads that extend beyond amplicon boundaries and use my amplicon info file</option> |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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68 </param> |
8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
parents:
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69 <when value="yes_compute" /> |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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70 <when value="yes"> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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71 <param name="amplicon_info" argument="-f" type="data" format="tabular" /> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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72 </when> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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73 <when value="" /> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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74 </conditional> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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75 <param name="primer_pos_wiggle" argument="-x" type="integer" min="0" value="0" |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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76 label="Wiggling room for read ends relative to primer binding sites" |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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|
77 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)" /> |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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78 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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79 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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|
80 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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81 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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82 </inputs> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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83 <outputs> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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84 <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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85 </outputs> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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86 <tests> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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87 <!-- #1: SARS-Cov data--> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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88 <test> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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89 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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90 <param name="input_bed" value="covid19/ARTIC-V1.bed" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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91 <param name="inc_primers" value="true" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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92 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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93 </test> |
4
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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94 <test> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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95 <!-- Test with primer bed file that needs to be sanitized --> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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96 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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97 <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" /> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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98 <param name="inc_primers" value="true" /> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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99 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> |
db536ad45f28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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100 </test> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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101 <!-- #1: Zika data--> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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102 <test> |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
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103 <conditional name="primer"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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104 <param name="source" value="history" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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105 <param name="input_bed" value="zika/db/zika_primers.bed" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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106 </conditional> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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107 <param name="input_bam" value="zika/Z52_a.sorted.bam" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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108 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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109 </test> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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110 <test> |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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111 <conditional name="primer"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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112 <param name="source" value="history" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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113 <param name="input_bed" value="zika/db/zika_primers.bed" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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114 </conditional> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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115 <param name="input_bam" value="zika/Z52_b.sorted.bam" /> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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116 <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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117 </test> |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
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118 <test> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
0
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119 <conditional name="primer"> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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120 <param name="source" value="cached" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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121 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" /> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents:
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122 </conditional> |
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
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123 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" /> |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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124 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/> |
2
cb903c9dc33d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
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125 </test> |
8
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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126 <test> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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127 <conditional name="primer"> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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128 <param name="source" value="cached" /> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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129 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" /> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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130 </conditional> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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131 <conditional name="amplicons"> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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132 <param name="filter_by" value="yes_compute" /> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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133 </conditional> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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134 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" /> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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135 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" compare="sim_size" delta="100000"/> |
397e5f0eb3ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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136 </test> |
0
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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137 </tests> |
8858fa037a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
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138 <help><![CDATA[ |
5
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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139 iVar uses primer positions supplied in a BED file to soft clip primer |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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140 sequences from an aligned and sorted BAM file. Following this, the reads are |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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141 trimmed further based on a quality threshold. |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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142 |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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143 **Primer and Amplicon info** |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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144 |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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145 The tool requires information about primers and their binding sites in 6-column |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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146 BED format. The information from this file is used to decide whether any mapped |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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147 read in the BAM input ends with a primer sequence and should, thus, be |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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148 soft-clipped. |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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149 |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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150 Optionally, the tool can also discard reads that do not fully map to within any |
cf65217ad61c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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151 amplicon. Such reads are likely to be wet-lab or mapping artefacts and removing |
cf65217ad61c
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152 them can increase variant calling precision. To calculate the extent of |
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153 expected amplicons the tool requires an additional amplicon info dataset that |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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154 lists the names of primers that together form any given amplicon. Primer names |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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155 (exactly matching those in the primer info dataset) need to be TAB-separated |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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156 with one line per amplicon. |
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157 If the primer scheme has more than two primers contributing to a given amplicon |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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158 (in schemes using alternate primers), you can (in this Galaxy tool only) |
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159 specify all of them on one line and the tool will calculate the maximum extent |
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160 of the amplicon. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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161 |
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162 **Quality trimming details** |
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163 |
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164 To do the quality trimming, iVar uses a sliding window approach. The window |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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165 slides from the 5' end to the 3' end and if at any point the average base |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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166 quality in the window falls below the threshold, the remaining read is soft |
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167 clipped. If after trimming, the length of the read is greater than the minimum |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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168 length specified, the read is written to the new trimmed BAM file. |
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169 |
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170 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. |
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171 ]]></help> |
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172 <expand macro="citations" /> |
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173 </tool> |