Mercurial > repos > sanbi-uwc > lofreq

annotate lofreq_call.xml @ 6:c208346da4be draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0-dirty
author sanbi-uwc
date Wed, 20 Sep 2017 04:54:30 -0400
parents e4504b37b5c8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
1 <tool id="lofreq_call" name="LoFreq Calling Variants" version="0.1.0">
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
2 <requirements>
2
22dc4d7e66bf planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit d45c1e39f18268f21d9913ac43a9b436b0cc244d
sanbi-uwc
parents: 1
diff changeset
3 <requirement type="package" version="2.1.3.1">lofreq</requirement>
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
4 </requirements>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
5 <stdio>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
6 <exit_code range="1:" />
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
7 </stdio>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
8 <command><![CDATA[
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
9 lofreq call
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
10 -f "$input1"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
11 -o "$output1"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
12 #if $region and str($region) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
13 -r "$region"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
14 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
15 #if $RegionBedFile and str($RegionBedFile) != '':
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
16 -l "$RegionBedFile"
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
17 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
18 --min-bq "$MinBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
19 --min-alt-bq "$MinAltBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
20 --def-alt-bq "$DefAltBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
21 --min-jq "$MinJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
22 --min-alt-jq "$MinAltJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
23 --def-alt-jq "$DefAltJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
24 #if $BaseAlignmentAndIndedAlignment and str($BaseAlignmentAndIndedAlignment) != '':
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
25 #echo " "
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
26 #echo ' '.join(str($BaseAlignmentAndIndedAlignment).split(','))
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
27 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
28 --min-mq "$MinMq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
29 --max-mq "$MaxMq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
30 --def-nm-q "$DefNmQ"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
31 --min-cov "$MinCov"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
32 --max-depth "$MaxDepth"
5
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
33 --sig "$Sig"
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
34 --bonf "$Bonf"
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
35 --force-overwrite
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
36 $merge_mapping_quality
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
37 #if $sq_vcf and str($sq_vcf) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
38 -S "$sq_vcf"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
39 #end if
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
40 #if $indels and str($indels) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
41 #echo " "
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
42 #echo ' '.join(str($indels).split(','))
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
43 #end if
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
44 #if $misc and str($misc) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
45 #echo " "
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
46 #echo ' '.join(str($misc).split(','))
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
47 #end if
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
48 "$input2"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
49 ]]></command>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
50 <inputs>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
51 <param type="data" name="input2" format="bam" label="Input Bam File"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
52 <param type="data" name="input1" format="fa,fasta" label="Indexed reference fasta file (gzip supported)" help="Indexed reference fasta file (gzip supported)"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
53 <param name="region" type="text" label="Limit calls to this region (chrom:start-end)">
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
54 <help>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
55 Limit calls to this region (chrom:start-end).
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
56 </help>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
57 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
58 </param>
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
59 <param format="bed" name="RegionBedFile" type="data" optional="true" label="List of positions (chr pos) or regions (BED) file"/>
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
60 <param name="MinBq" type="integer" label="Skip any base with baseQ smaller than" value="6" help="Skip any base with baseQ smaller than [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
61 <param name="MinAltBq" type="integer" label="Skip alternate bases with baseQ smaller than" value="6" help=" Skip alternate bases with baseQ smaller than [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
62 <param name="DefAltBq" type="integer" label="Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep)" value="0" help="Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
63 <param name="MinJq" type="integer" label="Skip any base with joinedQ smaller than" value="0" help="Skip any base with joinedQ smaller than [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
64 <param name="MinAltJq" type="integer" label="Skip alternate bases with joinedQ smaller than" value="0" help="Skip alternate bases with joinedQ smaller than [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
65 <param name="DefAltJq" type="integer" label="Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)" value="0" help="Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)" />
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
66
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
67 <param name="BaseAlignmentAndIndedAlignment" type="select" display="checkboxes" multiple="true" label="Base-alignment (BAQ) and indel-aligment (IDAQ) qualities Options">
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
68 <option value="--no-baq">Disable use of base-alignment quality (BAQ)</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
69 <option value="--del-baq">Delete pre-existing BAQ values, i.e. compute even if already present in BAM</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
70 <option value="--no-ext-baq"> Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
71 </param>
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
72 <param name="MinMq" type="integer" label="Skip reads with mapping quality smaller than" value="0" help="Skip reads with mapping quality smaller than [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
73 <param name="MaxMq" type="integer" label="Cap mapping quality at " value="0" help="Cap mapping quality at [INT]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
74 <param name="DefNmQ" type="integer" label="If >= 0, then replace non-match base qualities with this default value [-1] " value="0" help=" If >= 0, then replace non-match base qualities with this default value [-1]" />
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
sanbi-uwc
parents: 0
diff changeset
75 <param name="MinCov" type="integer" label="Test only positions having at least this coverage " value="1" help="(note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)" />
5
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
76 <param name="MaxDepth" type="integer" label="Cap coverage at this depth" value="1000000" help="Cap coverage at this depth [1000000] [INT]" />
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
77
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
78 <param name="merge_mapping_quality" type="boolean" truevalue="" falsevalue="--no-mq" checked="true" label="Don't merge mapping quality in LoFreq's model"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
79 <param format="vcf" name="sq_vcf" type="data" optional="true" label="Ignore variants in this vcf file for source quality computation."/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
80 <param name="indels" type="select" display="checkboxes" multiple="true" label="Indels Options">
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
81 <option value="--call-indels">Enable indel calls (note: preprocess your file to include indel alignment qualities!)</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
82 <option value="--only-indels">Only call indels; no SNVs</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
83 </param>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
84
6
c208346da4be planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0-dirty
sanbi-uwc
parents: 5
diff changeset
85 <param name="Sig" type="float" label="P-Value cutoff / significance level [0.010000]" value="0.010000" help="P-Value cutoff / significance level [0.010000]" />
5
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
86 <param name="Bonf" type="text" label="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" value="dynamic" help="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" />
e4504b37b5c8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0
sanbi-uwc
parents: 4
diff changeset
87
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
88 <param name="misc" type="select" display="checkboxes" multiple="true" label="Misc Options">
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
89 <option value="--illumina-1.3">Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
90 <option value="--verbose">Be verbose</option>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
91 </param>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
92
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
93 </inputs>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
94 <outputs>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
95 <data name="output1" format="vcf" />
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
96 </outputs>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
97 <tests>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
98 <test>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
99 <param name="input1" value="ref.fa"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
100 <param name="input2" value="aln.bam"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
101 <output name="output1" file="vars.vcf"/>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
102 </test>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
103 </tests>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
104 <help><![CDATA[
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
105 lofreq call: call variants from BAM file
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
106
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
107 Usage: lofreq call [options] in.bam
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
108
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
109 Options:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
110 - Reference:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
111 -f | --ref FILE Indexed reference fasta file (gzip supported) [null]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
112 - Output:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
113 -o | --out FILE Vcf output file [- = stdout]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
114 - Regions:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
115 -r | --region STR Limit calls to this region (chrom:start-end) [null]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
116 -l | --bed FILE List of positions (chr pos) or regions (BED) [null]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
117 - Base-call quality:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
118 -q | --min-bq INT Skip any base with baseQ smaller than INT [6]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
119 -Q | --min-alt-bq INT Skip alternate bases with baseQ smaller than INT [6]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
120 -R | --def-alt-bq INT Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
121 -j | --min-jq INT Skip any base with joinedQ smaller than INT [0]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
122 -J | --min-alt-jq INT Skip alternate bases with joinedQ smaller than INT [0]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
123 -K | --def-alt-jq INT Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
124 - Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
125 -B | --no-baq Disable use of base-alignment quality (BAQ)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
126 -A | --no-idaq Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
127 -D | --del-baq Delete pre-existing BAQ values, i.e. compute even if already present in BAM
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
128 -e | --no-ext-baq Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
129 - Mapping quality:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
130 -m | --min-mq INT Skip reads with mapping quality smaller than INT [0]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
131 -M | --max-mq INT Cap mapping quality at INT [255]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
132 -N | --no-mq Don't merge mapping quality in LoFreq's model
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
133 - Indels:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
134 --call-indels Enable indel calls (note: preprocess your file to include indel alignment qualities!)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
135 --only-indels Only call indels; no SNVs
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
136 - Source quality:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
137 -s | --src-qual Enable computation of source quality
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
138 -S | --ign-vcf FILE Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
139 -T | --def-nm-q INT If >= 0, then replace non-match base qualities with this default value [-1]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
140 - P-values:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
141 -a | --sig P-Value cutoff / significance level [0.010000]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
142 -b | --bonf Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
143 - Misc.:
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
144 -C | --min-cov INT Test only positions having at least this coverage [1]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
145 (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
146 -d | --max-depth INT Cap coverage at this depth [1000000]
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
147 --illumina-1.3 Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
148 --use-orphan Count anomalous read pairs (i.e. where mate is not aligned properly)
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
149 --plp-summary-only No variant calling. Just output pileup summary per column
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
150 --no-default-filter Don't run default 'lofreq filter' automatically after calling variants
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
151 --force-overwrite Overwrite any existing output
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
152 --verbose Be verbose
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
153 --debug Enable debugging
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
154
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
155 ]]></help>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
156 <citations>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
157 <citation type="bibtex">
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
158 @misc{githublofreq,
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
159 author = {LastTODO, FirstTODO},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
160 year = {TODO},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
161 title = {lofreq},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
162 publisher = {GitHub},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
163 journal = {GitHub repository},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
164 url = {https://github.com/CSB5/lofreq},
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
165 }</citation>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
166 </citations>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
parents:
diff changeset
167 </tool>