Mercurial > repos > iuc > megan_daa_meganizer

annotate daa_meganizer.xml @ 0:ca7c839a75ab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:10:15 +0000
parents
children f1b6527ba952
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ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
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1 <tool id="megan_daa_meganizer" name="MEGAN: meganize a DIAMOND file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>for use with MEGAN</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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## daa-meganizer "meganizes" the input, altering
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10 ## the file itself instead of producing a separate
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11 ## output. We'll make a copy of the input to handle
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12 ## this issue. The input must also have a .daa file
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13 ## extension.
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14 #set input_identifier = 'input.' + $in.ext
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15 cp '${in}' '${input_identifier}' &&
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16
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17 daa-meganizer
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18 --in '${input_identifier}'
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19 #if $advanced_options.metaDataFile:
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20 --metaDataFile '$advanced_options.metaDataFile'
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21 #end if
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22 $advanced_options.longReads
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23 $advanced_options.classify
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24 --minScore $advanced_options.minScore
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25 --maxExpected $advanced_options.maxExpected
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26 --minPercentIdentity $advanced_options.minPercentIdentity
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27 --topPercent $advanced_options.topPercent
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28 --minSupportPercent $advanced_options.minSupportPercent
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29 --minSupport $advanced_options.minSupport
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30 --minPercentReadCover $advanced_options.minPercentReadCover
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31 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
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32 --minReadLength $advanced_options.minReadLength
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33 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
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34 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
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35 --readAssignmentMode '$advanced_options.readAssignmentMode'
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36 #if $advanced_options.conFile:
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37 --conFile '$advanced_options.conFile'
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38 #end if
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39 #if $advanced_options.mapDB:
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40 --mapDB '$advanced_options.mapDB'
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41 #end if
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42 #if str($advanced_options.only) != '':
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43 --only '$advanced_options.only'
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44 #end if
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45 --threads \${GALAXY_SLOTS:-8}
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46 --tempStoreDir '.'
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47 && mv '$input_identifier' '$output'
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48 ]]></command>
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49 <inputs>
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50 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
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51 <section name="advanced_options" title="Advanced options" expanded="false">
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52 <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
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53 <expand macro="long_reads_param"/>
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54 <expand macro="classify_param"/>
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55 <expand macro="blast_params"/>
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56 <expand macro="min_max_params"/>
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57 <expand macro="lca_params"/>
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58 <expand macro="read_assignment_mode_param"/>
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59 <expand macro="con_file_param"/>
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60 <expand macro="mapdb_param"/>
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61 <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
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62 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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63 </param>
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64 </section>
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65 </inputs>
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66 <outputs>
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67 <data name="output" format="daa"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="in" ftype="daa" value="input.daa"/>
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72 <output name="output" ftype="daa">
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73 <assert_contents>
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74 <has_size value="3500"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 </tests>
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79 <help>
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80 **What it does**
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81
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82 Meganizes a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
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83 for disk image files. The output is a DIAMOND file consisting of the original input file, but with additional blocks of
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84 information appended to the end of the file.
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85
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86 </help>
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87 <expand macro="citations"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
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88 </tool>