/var/lib/mobyle/programs/taxoptimizer.xml is in mobyle-programs 5.1.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 | <program>
<head>
<name>taxoptimizer</name>
<version>1.0</version>
<doc>
<title>taxoptimizer</title>
<description>
<text lang="en">taxoptimizer reports taxonomic information for each Blast HIT</text>
</description>
<authors>C. Maufrais</authors>
</doc>
<category>database:search:display</category>
<command>taxoptimizer</command>
</head>
<parameters>
<parameter issimple="1" ismandatory="1" ismaininput="1">
<name>inputFile</name>
<prompt>Blast Result input file</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<comment>
<text lang="en">Tabulated file</text>
</comment>
<format>
<code proglang="python">' -i ' + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<paragraph>
<prompt>Output Options</prompt>
<name>taxoptimizerOptions</name>
<parameters>
<parameter>
<name>columnNumber</name>
<prompt>Column number to parse (default second column: 2)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<comment>
<text lang="en">Column number to parse (default second column: 2)</text>
</comment>
<argpos>20</argpos>
<format>
<code proglang="python">' -c ' + str(value)</code>
</format>
<vdef>
<value>2</value>
</vdef>
</parameter>
<parameter>
<name>database</name>
<prompt>Specific database to reduce the query</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<comment>
<text lang="en">Specified Database name for finding taxonomy in only one database.</text>
</comment>
<argpos>40</argpos>
<format>
<code proglang="python"> ('',' -d '+ str(value))[value is not None]</code>
</format>
</parameter>
<parameter>
<name>description</name>
<prompt>Add description in output </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<argpos>70</argpos>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">('',' -e ')[value]</code>
</format>
<comment>
<text lang="en">Add description (DE) in output</text>
</comment>
</parameter>
<parameter issimple="1">
<name>OnlyTaxonomyInformation</name>
<prompt>Limit the output only to sequences with taxonomic information</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">Only write lines with taxonomy information in output file</text>
</comment>
<argpos>70</argpos>
<format>
<code proglang="python">('',' -x ')[value]</code>
</format>
</parameter>
<parameter issimple="1">
<name>NoTaxonomyInfo</name>
<prompt>Reports sequences with no taxo output in another output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">Outputs sequences with no taxonomic information</text>
</comment>
<argpos>80</argpos>
<filenames>
<code proglang="python">('',' -f ')[value]</code>
</filenames>
</parameter>
</parameters>
<layout>
<vbox>
<box>columnNumber</box>
<box>SeparatorCharacter</box>
<box>database</box>
<box>description</box>
<box>OnlyTaxonomyInformation</box>
<box>NoTaxonomyInfo</box>
</vbox>
</layout>
</paragraph>
<parameter ishidden="1">
<name>OutputFileName</name>
<prompt lang="en">Output File Name</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>taxoptimizer.out</value>
</vdef>
</parameter>
<parameter isout="1">
<name>OutputNoTaxonomy</name>
<prompt>SequencesWithNoTaxoOutput</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<comment>
<text lang="en">taxoptimizer secondary output</text>
</comment>
<argpos>85</argpos>
<precond>
<code proglang="python"> NoTaxonomyInfo is not None </code>
</precond>
<format>
<code proglang="python"> ' -f noTaxo' + OutputFileName</code>
</format>
<filenames>
<code proglang="python">"noTaxo"+ OutputFileName</code>
</filenames>
</parameter>
<parameter isstdout="1" >
<name>OutputFile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>taxoptimizerTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">OutputFileName</code>
</filenames>
<comment>
<text lang="en">Reports Taxonomic annotation and concatenates to blast results</text>
</comment>
<argpos>90</argpos>
<format>
<code proglang="python">' -o ' + OutputFileName</code>
</format>
</parameter>
</parameters>
</program>
|