Mercurial > repos > gga > chado_phylogeny_load_tree

annotate phylogeny_load_tree.xml @ 0:b44be6289549 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:42:08 -0400
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children 31f6e0f70e41
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1 <?xml version="1.0"?>
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2 <tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0">
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3 <description>for phylogeny module</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="chado.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @AUTH@
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11
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12 chakin phylogeny load_tree
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13 '$newick'
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14 '$analysis_id'
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15
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16 #if $name:
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17 --name '$name'
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18 #end if
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19 #if $xref_db:
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20 --xref_db '$xref_db'
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21 #end if
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22 #if $xref_accession:
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23 --xref_accession '$xref_accession'
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24 #end if
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25 #if $match_on_name:
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26 $match_on_name
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27 #end if
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28 #if $prefix:
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29 --prefix '$prefix'
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30 #end if
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31
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32 | jq -S . > $results
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33 ]]></command>
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34 <inputs>
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35 <!-- arguments -->
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36 <param name="newick" label="Newick" argument="newick" type="data" format="txt" help="Newick file to load (or directory containing multiple newick files to load)" />
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37 <param argument="--analysis_id"
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38 type="select"
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39 dynamic_options="list_analyses()"
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40 label="Analysis" />
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41
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42 <!-- options -->
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43 <param name="name" label="Name" argument="name" type="text" help="The name given to the phylotree entry in the database" />
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44 <param name="xref_db" label="Xref db" argument="xref_db" value="null" type="text" help="The name of the db to link dbxrefs for the trees" />
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45 <param name="xref_accession" label="Xref Accession" argument="xref_accession" type="text" help="The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified)" />
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46 <param name="match_on_name" label="Match On Name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match polypeptide features using their name instead of their uniquename" />
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47 <param name="prefix" label="Prefix" argument="prefix" type="text" help="Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)" />
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48 <expand macro="wait_for"/>
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49
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50 </inputs>
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51 <outputs>
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52 <data format="json" name="results"/>
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53 </outputs>
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54 <help>
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55 Load a phylogenetic tree (Newick format) into Chado db
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56
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57 @HELP@
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58 </help>
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59 </tool>