Mercurial > repos > iuc > lofreq_indelqual

annotate lofreq_indelqual.xml @ 2:f4473557ffc7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
author iuc
date Sat, 21 Mar 2020 10:51:47 -0400
parents 5d6a078d30b0
children 354b534eeab7
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5d6a078d30b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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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 #set $reference_source = $strategy.reference_source
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10 @PREPARE_REF@
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11 #end if
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12 lofreq indelqual
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13 #if $strategy.selector == 'dindel'
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14 --dindel
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15 --ref $reference_fasta_fn
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16 #else
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17 #if $strategy.deletions
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18 --uniform $strategy.insertions,$strategy.deletions
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19 #else
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20 --uniform $strategy.insertions
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21 #end if
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22 #end if
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23 -o output.bam $reads
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24 ]]></command>
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25 <inputs>
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26 <param type="data" name="reads" format="bam" label="Reads" />
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27 <conditional name="strategy">
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28 <param name="selector" type="select" label="Indel calculation approach">
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29 <option value="uniform">Uniform</option>
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30 <option value="dindel">Dindel</option>
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31 </param>
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32 <when value="uniform">
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33 <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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34 <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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35 </when>
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36 <when value="dindel">
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37 <expand macro="reference_interface" />
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="bam" from_work_dir="output.bam" label="Add indel qualities to data ${reads.dataset.hid}" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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47 <param name="selector" value="uniform" />
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48 <param name="insertions" value="20" />
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49 <param name="deletions" value="30" />
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50 <output name="output" file="indelqual-out1.bam" />
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51 </test>
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52 <test>
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53 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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54 <param name="selector" value="dindel" />
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55 <param name="ref_selector" value="history" />
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56 <param name="ref" ftype="fasta" value="pBR322.fa" />
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57 <output name="output" file="indelqual-out2.bam" />
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58 </test>
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59 <test>
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60 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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61 <param name="selector" value="uniform" />
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62 <param name="insertions" value="20" />
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63 <output name="output" file="indelqual-out3.bam" />
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 Insert indel qualities into BAM file
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68
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69 The tool has two modes: 'uniform' and 'dindel':
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70 - 'uniform' will assign a given value uniformly, whereas
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71 - 'dindel' will insert indel qualities based on Dindel.
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72
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73 Both will overwrite any existing values. Do not realign your BAM file afterwards!
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74 ]]></help>
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75 <expand macro="citations">
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76 <citation type="doi">10.1101/gr.112326.110</citation>
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77 </expand>
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78 </tool>