Mercurial > repos > sanbi-uwc > lofreq

annotate lofreq_call.xml @ 1:fe68e1ac1290 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
author sanbi-uwc
date Wed, 06 Sep 2017 23:46:47 -0400
parents 022deab2faf6
children 22dc4d7e66bf
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022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
sanbi-uwc
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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
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2 <requirements>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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3 <requirement type="package" version="2.1.2">lofreq</requirement>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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4 </requirements>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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8 <command><![CDATA[
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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9 lofreq call
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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10 -f "$input1"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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11 -o "$output1"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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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
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13 -r "$region"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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14 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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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
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16 -l "$RegionBedFile"
0
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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17 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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18 --min-bq "$MinBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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19 --min-alt-bq "$MinAltBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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20 --def-alt-bq "$DefAltBq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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21 --min-jq "$MinJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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22 --min-alt-jq "$MinAltJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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23 --def-alt-jq "$DefAltJq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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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
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25 #echo " "
1
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26 #echo ' '.join(str($BaseAlignmentAndIndedAlignment).split(','))
0
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27 #end if
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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28 --min-mq "$MinMq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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29 --max-mq "$MaxMq"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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30 --def-nm-q "$DefNmQ"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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31 --min-cov "$MinCov"
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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32 --max-depth "$MaxDepth"
0
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33 $merge_mapping_quality
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34 #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
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35 -S "$sq_vcf"
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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36 #end if
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37 #if $indels and str($indels) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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38 #echo " "
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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39 #echo ' '.join(str($indels).split(','))
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40 #end if
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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41 #if $misc and str($misc) != '':
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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42 #echo " "
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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43 #echo ' '.join(str($misc).split(','))
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44 #end if
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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45 "$input2"
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46 ]]></command>
022deab2faf6 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5b7700f349511e79316cd2ebc2d27eb7c11398e4
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47 <inputs>
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48 <param type="data" name="input2" format="bam" label="Input Bam File"/>
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49 <param type="data" name="input1" format="fa,fasta" label="Indexed reference fasta file (gzip supported)" help="Indexed reference fasta file (gzip supported)"/>
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50 <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
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51 <help>
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52 Limit calls to this region (chrom:start-end).
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53 </help>
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54 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
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55 </param>
1
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56 <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
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57 <param name="MinBq" type="integer" label="Skip any base with baseQ smaller than" value="6" help="Skip any base with baseQ smaller than [INT]" />
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58 <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
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59 <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
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60 <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
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61 <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
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62 <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
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63
1
fe68e1ac1290 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit bae33ff4832e61fd4f4f9c3c52116d320299625a
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64 <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
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65 <option value="--no-baq">Disable use of base-alignment quality (BAQ)</option>
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66 <option value="--no-idap">Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)</option>
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67 <option value="--del-baq">Delete pre-existing BAQ values, i.e. compute even if already present in BAM</option>
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68 <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
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69 </param>
1
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70 <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
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71 <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
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72 <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
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73 <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)" />
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74 <param name="MaxDepth" type="integer" label=" Cap coverage at this depth" value="1000000" help="Cap coverage at this depth [1000000] [INT]" />
0
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75
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76 <param name="merge_mapping_quality" type="boolean" truevalue="" falsevalue="--no-mq" checked="true" label="Don't merge mapping quality in LoFreq's model"/>
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77 <param format="vcf" name="sq_vcf" type="data" optional="true" label="Ignore variants in this vcf file for source quality computation."/>
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78 <param name="indels" type="select" display="checkboxes" multiple="true" label="Indels Options">
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79 <option value="--call-indels">Enable indel calls (note: preprocess your file to include indel alignment qualities!)</option>
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80 <option value="--only-indels">Only call indels; no SNVs</option>
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81 </param>
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82
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83 <param name="misc" type="select" display="checkboxes" multiple="true" label="Misc Options">
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84 <option value="--src-qual">Enable computation of source quality</option>
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85 <option value="--sig">P-Value cutoff / significance level [0.010000]</option>
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86 <option value="--bonf">Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']</option>
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87 <option value="--illumina-1.3">Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded</option>
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88 <option value="--use-orphan">Count anomalous read pairs (i.e. where mate is not aligned properly)</option>
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89 <option value="--plp-summary-only">No variant calling. Just output pileup summary per column</option>
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90 <option value="--no-default-filter">Don't run default 'lofreq filter' automatically after calling variants</option>
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91 <option value="--force-overwrite">Overwrite any existing output</option>
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92 <option value="--verbose">Be verbose</option>
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93 <option value="--debug">Enable debugging</option>
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94 </param>
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95
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96 </inputs>
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97 <outputs>
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98 <data name="output1" format="vcf" />
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input1" value="ref.fa"/>
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103 <param name="input2" value="aln.bam"/>
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104 <output name="output1" file="vars.vcf"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 lofreq call: call variants from BAM file
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109
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110 Usage: lofreq call [options] in.bam
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111
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112 Options:
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113 - Reference:
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114 -f | --ref FILE Indexed reference fasta file (gzip supported) [null]
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115 - Output:
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116 -o | --out FILE Vcf output file [- = stdout]
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117 - Regions:
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118 -r | --region STR Limit calls to this region (chrom:start-end) [null]
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119 -l | --bed FILE List of positions (chr pos) or regions (BED) [null]
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120 - Base-call quality:
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121 -q | --min-bq INT Skip any base with baseQ smaller than INT [6]
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122 -Q | --min-alt-bq INT Skip alternate bases with baseQ smaller than INT [6]
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123 -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]
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124 -j | --min-jq INT Skip any base with joinedQ smaller than INT [0]
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125 -J | --min-alt-jq INT Skip alternate bases with joinedQ smaller than INT [0]
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126 -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]
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127 - Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
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128 -B | --no-baq Disable use of base-alignment quality (BAQ)
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129 -A | --no-idaq Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
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130 -D | --del-baq Delete pre-existing BAQ values, i.e. compute even if already present in BAM
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131 -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)
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132 - Mapping quality:
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133 -m | --min-mq INT Skip reads with mapping quality smaller than INT [0]
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134 -M | --max-mq INT Cap mapping quality at INT [255]
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135 -N | --no-mq Don't merge mapping quality in LoFreq's model
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136 - Indels:
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137 --call-indels Enable indel calls (note: preprocess your file to include indel alignment qualities!)
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138 --only-indels Only call indels; no SNVs
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139 - Source quality:
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140 -s | --src-qual Enable computation of source quality
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141 -S | --ign-vcf FILE Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
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142 -T | --def-nm-q INT If >= 0, then replace non-match base qualities with this default value [-1]
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143 - P-values:
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144 -a | --sig P-Value cutoff / significance level [0.010000]
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145 -b | --bonf Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
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146 - Misc.:
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147 -C | --min-cov INT Test only positions having at least this coverage [1]
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148 (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
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149 -d | --max-depth INT Cap coverage at this depth [1000000]
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150 --illumina-1.3 Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
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151 --use-orphan Count anomalous read pairs (i.e. where mate is not aligned properly)
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152 --plp-summary-only No variant calling. Just output pileup summary per column
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153 --no-default-filter Don't run default 'lofreq filter' automatically after calling variants
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154 --force-overwrite Overwrite any existing output
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155 --verbose Be verbose
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156 --debug Enable debugging
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157
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158 ]]></help>
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159 <citations>
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160 <citation type="bibtex">
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161 @misc{githublofreq,
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162 author = {LastTODO, FirstTODO},
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163 year = {TODO},
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164 title = {lofreq},
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165 publisher = {GitHub},
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166 journal = {GitHub repository},
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167 url = {https://github.com/CSB5/lofreq},
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168 }</citation>
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169 </citations>
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170 </tool>