Mercurial > repos > earlhaminst > ete

annotate ete_homology_classifier.xml @ 8:16e925bf567e draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author earlhaminst
date Thu, 31 Oct 2019 07:48:59 -0400
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1 <tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@">
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16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
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2 <description>from a genetree using the ETE Toolkit</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
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5 <xml name="homologies_macro" token_label="" token_help="">
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6 <param name="homologies" type="select" multiple="true" optional="false" display="checkboxes" label="@LABEL@" help="@HELP@">
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7 <option value="one-to-one" selected="true">one-to-one</option>
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8 <option value="one-to-many" selected="true">one-to-many</option>
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9 <option value="many-to-one" selected="true">many-to-one</option>
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10 <option value="many-to-many" selected="true">many-to-many</option>
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11 <option value="paralogs" selected="true">Paralogs</option>
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12 </param>
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13 </xml>
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14 </macros>
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15 <expand macro="requirements" />
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16 <command detect_errors="exit_code">
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17 <![CDATA[
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18 python '$__tool_directory__/ete_homology_classifier.py'
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19 --genetree '$genetreeFile'
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20 --out_format '$format_type.out_format'
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21 #if $format_type.homologies:
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22 --filters $format_type.homologies
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23 #end if
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24 > $homology
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
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29 <conditional name="format_type">
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30 <param name="out_format" type="select" label="Output format">
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31 <option value="tabular" selected="true">Tabular</option>
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32 <option value="csv">One-line CSV</option>
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33 </param>
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34 <when value="tabular">
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35 <expand macro="homologies_macro" label="Pair types to keep"/>
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36 </when>
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37 <when value="csv">
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38 <expand macro="homologies_macro" label="Allowed homology types for the GeneTree" help="If the GeneTree contains any other homology type, then the output will be empty" />
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39 </when>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data format="tabular" name="homology" label="${tool.name} on ${on_string}">
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44 <change_format>
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45 <when input="format_type.out_format" value="csv" format="csv" />
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46 </change_format>
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47 </data>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
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52 <param name="out_format" value="tabular"/>
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53 <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
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54 <output name="homology" file="11_homology.tabular" />
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55 </test>
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56 <test>
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57 <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" />
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58 <param name="out_format" value="csv"/>
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59 <output name="homology" file="11_homology.csv" />
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64 Classify and filter Homology from single GeneTree by utilising the `ETE Toolkit`_.
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65
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66 .. _ETE Toolkit: http://etetoolkit.org/
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67
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68 **Output format:**
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69
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70 *tabular*:
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71
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72 ====================== ======================== ============
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73 gene_1 gene_2 homology
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74 ====================== ======================== ============
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75 insr_rattusnorvegicus insr_musmusculus one-to-one
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76 insr_rattusnorvegicus insr_homosapiens one-to-one
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77 insr_rattusnorvegicus insr_pantroglodytes one-to-one
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78 insr_rattusnorvegicus insr_susscrofa one-to-one
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79 insr_musmusculus insr_homosapiens one-to-one
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80 insr_musmusculus insr_pantroglodytes one-to-one
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81 insr_musmusculus insr_susscrofa one-to-one
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82 insr_homosapiens insr_pantroglodytes one-to-one
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83 insr_homosapiens insr_susscrofa one-to-one
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84 insr_pantroglodytes insr_susscrofa one-to-one
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85 ====================== ======================== ============
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86
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87 \
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88
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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89 *One-line CSV*::
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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90
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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91 insr_rattusnorvegicus,insr_musmusculus,insr_homosapiens,insr_pantroglodytes,insr_susscrofa
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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92 ]]>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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93 </help>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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94 <expand macro="citations" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
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95 </tool>