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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 15:24:44 +0000
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d1b53ef02092 "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_alnqual" name="Add BAQ and IDAQ" version="@WRAPPER_VERSION@0">
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2 <description>to BAM with LoFreq</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 @PREPARE_REF@
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9 lofreq alnqual -b $extended $no_baq $no_idaq $recompute_all '$reads' '$reference_fasta_fn' > '$output'
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10 ]]></command>
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11 <inputs>
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12 <param type="data" name="reads" format="bam" />
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13 <expand macro="reference_interface" />
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14 <param name="extended" argument="-e" type="boolean" truevalue="-e" falsevalue="" label="Use default instead of extended BAQ" help="Extended BAQ gives better sensitivity with lower specificity" />
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15 <param name="no_baq" argument="-B" type="boolean" truevalue="-B" falsevalue="" label="Skip base alignment quality calculation" />
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16 <param name="no_idaq" argument="-A" type="boolean" truevalue="-A" falsevalue="" label="Skip indel alignment quality calculation" />
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17 <param name="recompute_all" argument="-r" type="boolean" truevalue="-r" falsevalue="" label="Overwrite existing values with computed values" />
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="bam" label="${tool.name} to ${on_string}" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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25 <param name="ref_selector" value="history" />
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26 <param name="ref" ftype="fasta" value="pBR322.fa" />
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27 <output name="output" file="alnqual-out1.bam" />
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28 </test>
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29 <test>
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30 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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31 <param name="ref_selector" value="history" />
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32 <param name="ref" ftype="fasta" value="pBR322.fa" />
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33 <param name="no_baq" value="true" />
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34 <output name="output" file="alnqual-out2.bam" />
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35 </test>
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36 <test>
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37 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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38 <param name="ref_selector" value="history" />
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39 <param name="ref" ftype="fasta" value="pBR322.fa" />
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40 <param name="no_idaq" value="true" />
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41 <output name="output" file="alnqual-out3.bam" />
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42 </test>
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43 <test>
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44 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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45 <param name="ref_selector" value="history" />
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46 <param name="ref" ftype="fasta" value="pBR322.fa" />
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47 <param name="extended" value="true" />
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48 <output name="output" file="alnqual-out4.bam" />
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49 </test>
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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="ref_selector" value="history" />
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53 <param name="ref" ftype="fasta" value="pBR322.fa" />
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54 <param name="recompute" value="true" />
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55 <output name="output" file="alnqual-out5.bam" />
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to BAM file
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60
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61 Usage: lofreq alnqual [options] <aln.bam> <ref.fasta>
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62 Options:
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63 -b BAM output (instead of SAM)
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64 -u Uncompressed BAM output (for piping)
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65 -S The input is SAM with header
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66 -e Use default instead of extended BAQ (the latter gives better sensitivity but lower specificity)
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67 -B Don't compute base alignment qualities
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68 -A Don't compute indel alignment qualities
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69 -r Recompute i.e. overwrite existing values
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70 - Output BAM will be written to stdout.
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71 - Only reads containing indels will contain indel-alignment qualities (tags: ai and ad).
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72 - Do not change the alignmnent after running this, i.e. use this as last postprocessing step!
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73 - This program is based on samtools. BAQ was introduced by Heng Li PMID:21320865
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74
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75
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>