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comparison ete_lineage_generator.xml @ 6:f1eca1158f21 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
author earlhaminst
date Wed, 10 Oct 2018 05:24:04 -0400
parents 87b6de3ef63e
children 2db72467da51
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5:817031b8486d 6:f1eca1158f21
18 #end if 18 #end if
19 #if $compresscond.compress == "-c" 19 #if $compresscond.compress == "-c"
20 $compresscond.compress 20 $compresscond.compress
21 $compresscond.lower 21 $compresscond.lower
22 #end if 22 #end if
23 $includeid
23 ]]></command> 24 ]]></command>
24 <inputs> 25 <inputs>
25 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species/taxid per line" /> 26 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species/taxid per line" />
26 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" /> 27 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
27 <conditional name="ranks"> 28 <conditional name="ranks">
66 <when value="primary" /> 67 <when value="primary" />
67 <when value="full" /> 68 <when value="full" />
68 </conditional> 69 </conditional>
69 <conditional name="compresscond"> 70 <conditional name="compresscond">
70 <param name="compress" type="select" label="Fill unnamed ranks" help="Fill unnamed ranks with super/sub ranks (see -l)"> 71 <param name="compress" type="select" label="Fill unnamed ranks" help="Fill unnamed ranks with super/sub ranks (see -l)">
71 <option value="-c">Yes</option> 72 <option value="-c" selected="True">Yes</option>
72 <option value="">No</option> 73 <option value="">No</option>
73 </param> 74 </param>
74 <when value="-c"> 75 <when value="-c">
75 <param name="lower" type="select" label="Prefer lower ranks for filling" help="Prefer lower levels for filling"> 76 <param name="lower" type="boolean" truevalue="-l" falsevalue="" checked="False" label="Prefer lower ranks" help="Take the next available lower rank (default: higher)"/>
76 <option value="-l">Yes</option>
77 <option value="">No</option>
78 </param>
79 </when> 77 </when>
80 <when value="" /> 78 <when value="" />
81 </conditional> 79 </conditional>
80 <param name="includeid" type="boolean" truevalue="--includeid" falsevalue="" label="Include taxid in the table"
81 help="For the case when the input consists of taxon names" />
82 </inputs> 82 </inputs>
83 <outputs> 83 <outputs>
84 <data name="outputFile" format="tsv" label="${tool.name} on ${on_string}"/> 84 <data name="outputFile" format="tsv" label="${tool.name} on ${on_string}"/>
85 </outputs> 85 </outputs>
86 <tests> 86 <tests>
112 <param name="compress" value="" /> 112 <param name="compress" value="" />
113 <param name="levels" value="manual" /> 113 <param name="levels" value="manual" />
114 <param name="manualranks" value="kingdom,family" /> 114 <param name="manualranks" value="kingdom,family" />
115 <output name="outputFile" file="lineage-full.txt" /> 115 <output name="outputFile" file="lineage-full.txt" />
116 </test> 116 </test>
117 <test>
118 <param name="speciesFile" ftype="txt" value="species.txt" />
119 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
120 <param name="includeid" value="--includeid" />
121 <output name="outputFile" file="lineage-wid.txt" />
122 </test>
117 </tests> 123 </tests>
118 <help><![CDATA[ 124 <help><![CDATA[
119 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_. 125 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.
120 126
121 .. _ETE Toolkit: http://etetoolkit.org/ 127 .. _ETE Toolkit: http://etetoolkit.org/