Mercurial > repos > iuc > megan_daa2rma

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 6b0c3dbd5bdf9c272cf32f39e0004d504f953ff0
author iuc
date Sat, 27 Aug 2022 17:04:50 +0000
parents 10360f9989ee
children
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0
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1 <tool id="megan_daa2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from a DIAMOND daa 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="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 #set input_identifier = 'input.' + $in.ext
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10 ln -s '${in}' '${input_identifier}' &&
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11
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12 daa2rma
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13 --in '${input_identifier}'
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14 #if $advanced_options.metaDataFile:
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15 --metaDataFile '$advanced_options.metaDataFile'
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16 #end if
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17 #if str($advanced_options.paired_reads_cond.paired_reads) == 'yes':
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18 --paired
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19 $advanced_options.paired_reads_cond.pairedSuffixLength
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20 #end if
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21 $advanced_options.longReads
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22 --maxMatchesPerRead $advanced_options.maxMatchesPerRead
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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 $advanced_options.lcaCoveragePercent
e13ac00e6a4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
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35 --readAssignmentMode '$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 --out '$output'
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46 --threads \${GALAXY_SLOTS:-8}
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47 --tempStoreDir '.'
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48 ]]></command>
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49 <inputs>
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50 <expand macro="input_daa_param"/>
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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 <conditional name="paired_reads_cond">
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54 <param name="paired_reads" type="select" label="DAA file was created using paired reads?">
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55 <option value="no" selected="true">no</option>
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56 <option value="yes">Yes</option>
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57 </param>
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58 <when value="no"/>
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59 <when value="yes">
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60 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
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61 </when>
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62 </conditional>
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63 <expand macro="long_reads_param"/>
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64 <expand macro="max_matches_per_read_param"/>
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65 <expand macro="classify_param"/>
1
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66 <expand macro="min_score_param"/>
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67 <expand macro="max_expected_param"/>
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68 <expand macro="min_percent_identity_param"/>
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69 <expand macro="top_percent_param"/>
0
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70 <expand macro="min_max_params"/>
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71 <expand macro="lca_params"/>
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72 <expand macro="read_assignment_mode_param"/>
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73 <expand macro="con_file_param"/>
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74 <expand macro="mapdb_param"/>
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75 <expand macro="only_named_classifications_param"/>
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76 </section>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="rma6"/>
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80 </outputs>
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81 <tests>
1
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82 <test expect_num_outputs="1">
0
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83 <param name="in" ftype="daa" value="input.daa"/>
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84 <output name="output" ftype="rma6">
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85 <assert_contents>
2
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86 <has_size value="1487" delta="25"/>
0
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87 </assert_contents>
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88 </output>
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89 </test>
1
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90 <test expect_num_outputs="1">
0
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91 <param name="in" ftype="daa" value="input.daa"/>
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92 <param name="longReads" value="true"/>
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93 <param name="minScore" value="25.0"/>
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94 <param name="maxExpected" value="0.05"/>
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95 <param name="lcaAlgorithm" value="weighted"/>
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96 <output name="output" ftype="rma6">
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97 <assert_contents>
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98 <has_size value="1445" delta="25"/>
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99 </assert_contents>
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100 </output>
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101 </test>
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102 </tests>
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103 <help>
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104 **What it does**
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105
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106 Generates a MEGAN RMA (RealMedia Audio) file from a DIAMOND DAA file, a proprietary file format developed by PowerISO Computing
0
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107 for disk image files. MEGAN uses an update of the original RMA file format known as RMA6.
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108 </help>
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109 <expand macro="citations"/>
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110 </tool>