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annotate lofreq_indelqual.xml @ 0:8d8ee5939303 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
author dave
date Wed, 27 Nov 2019 15:25:08 +0000
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8d8ee5939303 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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1 <tool id="lofreq_indelqual" name="Insert indel qualities" version="@WRAPPER_VERSION@0">
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2 <description>into a BAM file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $strategy.selector == 'dindel'
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9 #if str($strategy.reference_source.ref_selector) == 'history':
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10 #set $reference_fasta_fn = 'reference.fa'
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11 ln -s '$strategy.reference_source.ref' $reference_fasta_fn &&
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12 lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
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13 #else
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14 #set $reference_fasta_fn = str($strategy.reference_source.ref.fields.path)
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15 #end if
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16 #end if
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17 lofreq indelqual
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18 #if $strategy.selector == 'dindel'
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19 --dindel
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20 --ref $reference_fasta_fn
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21 #else
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22 #if $strategy.deletions
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23 --uniform $strategy.insertions,$strategy.deletions
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24 #else
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25 --uniform $strategy.insertions
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26 #end if
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27 #end if
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28 -o output.bam $reads
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29 ]]></command>
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30 <inputs>
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31 <param type="data" name="reads" format="bam" />
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32 <conditional name="strategy" label="Indel calculation approach">
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33 <param name="selector" type="select">
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34 <option value="uniform">Uniform</option>
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35 <option value="dindel">Dindel</option>
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36 </param>
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37 <when value="uniform">
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38 <param name="insertions" type="integer" value="30" label="Indel quality to add" help="Should probably not be left at the default value" />
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39 <param name="deletions" type="integer" optional="true" label="Separate deletion quality" help="Leave blank to use the same values for insertions and deletions" />
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40 </when>
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41 <when value="dindel">
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42 <expand macro="reference_interface" />
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data name="output" format="bam" from_work_dir="output.bam" label="Add indel qualities to data ${reads.dataset.hid}" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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52 <param name="selector" value="uniform" />
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53 <param name="insertions" value="20" />
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54 <param name="deletions" value="30" />
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55 <output name="output" file="indelqual-out1.bam" />
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56 </test>
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57 <test>
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58 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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59 <param name="selector" value="dindel" />
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60 <param name="ref_selector" value="history" />
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61 <param name="ref" ftype="fasta" value="pBR322.fa" />
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62 <output name="output" file="indelqual-out2.bam" />
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63 </test>
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64 <test>
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65 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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66 <param name="selector" value="uniform" />
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67 <param name="insertions" value="20" />
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68 <output name="output" file="indelqual-out3.bam" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 lofreq indelqual: Insert indel qualities into BAM file (required for indel predictions)
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73
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74 Usage: lofreq indelqual [options] in.bam
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75 Options:
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76 -u | --uniform INT[,INT] Add this indel quality uniformly to all bases.
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77 Use two comma separated values to specify
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78 insertion and deletion quality separately.
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79 (clashes with --dindel)
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80 --dindel Add Dindel's indel qualities (Illumina specific)
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81 (clashes with -u; needs --ref)
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82 -f | --ref Reference sequence used for mapping
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83 (Only required for --dindel)
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84 -o | --out FILE Output BAM file [- = stdout = default]
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85 --verbose Be verbose
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86
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87 The preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand.
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88 The command has two modes: 'uniform' and 'dindel':
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89 - 'uniform' will assign a given value uniformly, whereas
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90 - 'dindel' will insert indel qualities based on Dindel (PMID 20980555).
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91 Both will overwrite any existing values.
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92 Do not realign your BAM file afterwards!
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93
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94
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95 ]]></help>
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96 <expand macro="citations">
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97 <citation type="doi">10.1101/gr.112326.110</citation>
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98 </expand>
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99 </tool>