Mercurial > repos > iuc > lofreq_alnqual

annotate macros.xml @ 4:e0e2fd665102 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author iuc
date Mon, 15 Jun 2020 13:13:27 -0400
parents e61c9ac190ad
children
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1 <macros>
4
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2 <token name="@TOOL_VERSION@">2.1.5</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement>
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6 <yield/>
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7 </requirements>
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8 <version_command>lofreq version | grep version | cut -d ' ' -f 2</version_command>
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9 </xml>
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10 <xml name="citations">
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11 <citations>
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12 <citation type="doi">10.1093/nar/gks918</citation>
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13 <yield />
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14 </citations>
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15 </xml>
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16 <token name="@PREPARE_REF@"><![CDATA[
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17 #if str($reference_source.ref_selector) == 'history':
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18 #set $reference_fasta_fn = 'reference.fa'
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19 ln -s '$reference_source.ref' $reference_fasta_fn &&
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20 lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
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21 #else
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22 #set $reference_fasta_fn = str($reference_source.ref.fields.path)
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23 #end if
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24 ]]></token>
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25 <xml name="reference_interface">
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26 <conditional name="reference_source">
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27 <param name="ref_selector" type="select"
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28 label="Choose the source for the reference genome">
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29 <option value="cached">Locally cached</option>
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30 <option value="history">History</option>
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31 </param>
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32 <when value="cached">
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33 <param argument="--ref" type="select"
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34 label="Reference genome">
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35 <options from_data_table="fasta_indexes">
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36 <filter type="data_meta" column="dbkey" key="dbkey" ref="reads" />
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37 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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38 </options>
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39 </param>
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40 </when>
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41 <when value="history">
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42 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
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43 </when>
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44 </conditional>
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45 </xml>
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46 <xml name="handle_existing_alnqual">
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47 <conditional name="alnqual_choice">
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48 <param name="alnquals_to_use" type="select"
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49 label="Use the following alignment quality scores">
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50 <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
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51 <option value="-A">Only base alignment qualities (BAQ)</option>
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52 <option value="-B">Only indel alignment qualities (IDAQ)</option>
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53 </param>
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54 <when value="-B">
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55 <param name="extended_baq" type="hidden" value="" />
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56 </when>
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57 <when value="">
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58 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
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59 label="If BAQ needs to be computed, calculate extended BAQ?" />
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60 </when>
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61 <when value="-A">
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62 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
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63 label="If BAQ needs to be computed, calculate extended BAQ?" />
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64 </when>
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65 </conditional>
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66 </xml>
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67 <xml name="handle_alnqual" token_mode="Use">
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68 <conditional name="alnqual_choice">
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69 <param name="alnquals_to_use" type="select"
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70 label="@MODE@ the following alignment quality scores">
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71 <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
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72 <option value="-A">Only base alignment qualities (BAQ)</option>
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73 <option value="-B">Only indel alignment qualities (IDAQ)</option>
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74 </param>
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75 <when value="-B">
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76 <param name="extended_baq" type="hidden" value="" />
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77 </when>
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78 <when value="">
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79 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
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80 label="Use extended BAQ?" />
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81 </when>
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82 <when value="-A">
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83 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
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84 label="Use extended BAQ?" />
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85 </when>
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86 </conditional>
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87 </xml>
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88 </macros>