Mercurial > repos > earlhaminst > ete
comparison ete_lineage_generator.xml @ 6:f1eca1158f21 draft
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/ |