Mercurial > repos > iuc > megan_daa2info

annotate macros.xml @ 1:9cb0534a9829 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
author iuc
date Tue, 07 Dec 2021 10:16:38 +0000
parents 2f8df8e575f2
children c90a645ff6e9
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1 <macros>
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2 <token name="@TOOL_VERSION@">6.21.7</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">20.09</token>
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5 <xml name="bio_tools">
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6 <xrefs>
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7 <xref type="bio.tools">megan</xref>
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8 </xrefs>
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9 </xml>
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
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13 </requirements>
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14 </xml>
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15 <macro name="input_type_cond">
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16 <conditional name="input_type_cond">
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17 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
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18 <option value="single" selected="true">Single dataset</option>
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19 <option value="pair">Dataset pair</option>
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20 <option value="paired">List of dataset pairs</option>
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21 </param>
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22 <when value="single">
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23 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
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24 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
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25 </when>
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26 <when value="pair">
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27 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
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28 <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
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29 <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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30 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
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31 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
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32 </when>
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33 <when value="paired">
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34 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
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35 <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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36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
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37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
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38 </when>
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39 </conditional>
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40 </macro>
1
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41 <macro name="input_daa_param">
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42 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
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43 </macro>
0
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44 <macro name="long_reads_param">
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45 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
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46 </macro>
1
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47 <macro name="max_matches_per_read_param">
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48 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
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49 </macro>
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50 <macro name="only_named_classifications_param">
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51 <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
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52 <sanitizer>
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53 <valid initial="@VALIDINITIAL@">
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54 <remove value="&apos;" />
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55 <add value="|" />
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56 </valid>
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57 <mapping initial="none">
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58 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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59 </mapping>
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60 </sanitizer>
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61 </param>
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62 </macro>
0
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63 <macro name="classification_options">
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64 <option value="EC" selected="true">EC</option>
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65 <option value="EGGNOG">EGGNOG</option>
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66 <option value="GTDB">GTDB</option>
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67 <option value="INTERPRO2GO">INTERPRO2GO</option>
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68 <option value="KEGG">KEGG</option>
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69 <option value="SEED">SEED</option>
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70 <option value="Taxonomy">Taxonomy</option>
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71 </macro>
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72 <macro name="blast_mode_options">
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73 <option value="Unknown" selected="true">Unknown</option>
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74 <option value="BlastN">BlastN</option>
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75 <option value="BlastP">BlastP</option>
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76 <option value="BlastX">BlastX</option>
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77 <option value="Classifier">Classifier</option>
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78 </macro>
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79 <macro name="classify_param">
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80 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
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81 </macro>
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82 <macro name="blast_params">
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83 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
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84 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
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85 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
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86 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
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87 </macro>
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88 <macro name="min_max_params">
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89 <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
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90 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
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91 <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
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92 <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
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93 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
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94 </macro>
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95 <macro name="lca_params">
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96 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
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97 <option value="naive" selected="true">naive</option>
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98 <option value="weighted">weighted</option>
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99 <option value="longReads">longReads</option>
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100 </param>
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101 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
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102 </macro>
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103 <macro name="read_assignment_mode_param">
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104 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
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105 <option value="alignedBases" selected="true">alignedBases</option>
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106 <option value="readCount">readCount</option>
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107 </param>
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108 </macro>
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109 <macro name="con_file_param">
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110 <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>
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111 </macro>
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112 <macro name="mapdb_param">
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113 <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
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114 </macro>
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115 <xml name="sanitize_query" token_validinitial="string.printable">
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116 <sanitizer>
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117 <valid initial="@VALIDINITIAL@">
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118 <remove value="&apos;" />
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119 <add value="|" />
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120 </valid>
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121 <mapping initial="none">
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122 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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123 </mapping>
1
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124 </sanitizer>
0
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125 </xml>
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126 <xml name="citations">
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127 <citations>
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128 <citation type="doi">10.1038/nmeth.3176</citation>
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129 <citation type="doi">10.1101/gr.120618.111</citation>
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130 <citation type="doi">10.1101/gr.5969107</citation>
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131 </citations>
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132 </xml>
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133 </macros>
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134