Mercurial > repos > gga > chado_phylogeny_load_tree

annotate phylogeny_load_tree.xml @ 11:8f3b6bb4c05c draft

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author gga
date Tue, 05 Mar 2019 05:12:24 -0500
parents 2e38005d5205
children 4812a8770a8c
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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 #if $input.input_type == "archive":
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13 mkdir 'newick_arch/' &&
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14 tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
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15 #end if
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17 chakin phylogeny load_tree
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19 $match_on_name
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21 #if $prefix:
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22 --prefix '$prefix'
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23 #end if
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25 #if $xref_db:
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26 --xref_db '$xref_db'
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27 #end if
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29 #if $input.input_type == "archive":
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30 #if $name:
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31 --name '$name'
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32 #end if
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34 #if $xref_accession:
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35 --xref_accession '$xref_accession'
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36 #end if
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38 '$newick'
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39 #else
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40 'newick_arch/'
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41 #end if
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43 '$analysis_id'
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44
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45 | jq -S . > '$results'
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46 ]]></command>
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47 <inputs>
8
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48 <param argument="analysis_id"
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49 type="select"
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50 dynamic_options="list_analyses()"
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51 label="Analysis" />
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52
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53 <conditional name="input">
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54 <param name="input_type" type="select" label="Input type">
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55 <option value="file" selected="true">Newick file</option>
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56 <option value="archive">Tar.gz archive of Newick files</option>
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57 </param>
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58 <when value="file">
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59 <param name="newick" label="Newick" argument="newick" type="data" format="newick" help="Newick file to load" />
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60 <param name="name" label="Name" argument="--name" type="text" help="The name given to the phylotree entry in the database" />
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61 <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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62 </when>
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63 <when value="archive">
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64 <param name="newick_arch" label="Newicks archive" type="data" format="tar" help="Archive of Newick files to load (must be at the root of the archive)" />
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65 </when>
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66 </conditional>
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67
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68 <!-- options -->
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69 <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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70 <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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71 <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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72 <expand macro="wait_for"/>
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73
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74 </inputs>
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75 <outputs>
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76 <data format="json" name="results"/>
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77 </outputs>
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78 <help>
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79 Load a phylogenetic tree (Newick format) into Chado db
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80
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81 @HELP@
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82 </help>
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83 </tool>