Mercurial > repos > gga > tripal_analysis_load_go

annotate analysis_load_go.xml @ 7:daf9fbb01910 draft default tip

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author gga
date Wed, 14 Aug 2019 09:52:48 -0400
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1 <?xml version="1.0"?>
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2 <tool id="analysis_load_go" profile="16.04" name="Load Blast2GO results" version="@WRAPPER_VERSION@.0">
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3 <description>into Tripal</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="tripal.py"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
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13 &&
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15 cp '${input}' "\${tmp_dir}/blast2go.gaf"
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17 &&
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19 @AUTH@
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21 tripaille analysis load_go
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22
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23 --organism_id '${organism}'
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24
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25 @ANALYSIS@
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27 #if str($matching.query_re):
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28 --re_name '${matching.query_re}'
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29 #end if
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30
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31 #if $matching.query_uniquename:
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32 --query_matching 'uniquename'
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33 #else
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34 --query_matching 'uniquename'
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35 #end if
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36
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37 --query_type '$matching.query_type'
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38
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39 "\${tmp_dir}/blast2go.gaf"
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41 &&
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42
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43 echo "Data loaded" > '$results'
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44 ]]></command>
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45 <inputs>
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46 <param name="input"
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47 type="data"
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48 format="txt"
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49 label="Blast2Go results (GAF file)" />
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50
3
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51 <param argument="--organism"
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52 type="select"
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53 dynamic_options="list_organisms()"
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54 label="Organism" />
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55
0
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56 <expand macro="matching"/>
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57 <expand macro="analysis" />
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58 <expand macro="wait_for"/>
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59 </inputs>
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60 <outputs>
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61 <data format="txt" name="results" label="Load Blast2GO results into Tripal" />
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62 </outputs>
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63 <tests>
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64 <test expect_failure="true" expect_exit_code="1">
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65 <param name="input" value="blast2go.gaf" />
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66 <param name="query_type" value="polypeptide" />
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67 <param name="query_uniquename" value="true" />
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68 <section name="analysis">
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69 <param name="name" value="Some analysis" />
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70 <param name="program" value="interproscan" />
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71 <param name="program_version" value="58.2" />
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72 <param name="algorithm" value="blast2go" />
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73 <param name="source" value="NCBI" />
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74 <param name="source_version" value="1.0" />
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75 <param name="source_uri" value="http://ncbi.com/somewhere" />
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76 <param name="description" value="My cool new test analysis" />
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77 <param name="date" value="2016-12-12" />
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78 </section>
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79
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80 <expand macro="test_result" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 @HELP_OVERVIEW@
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85
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86 **Load Blast2Go results**
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87
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88 With this tool, you can load Blast2go results into the Tripal/Chado database.
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89
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90 A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.
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91
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92 The `tripal_analysis_go <http://github.com/tripal/tripal_analysis_go>`_ module must be installed and configured on the Tripal instance.
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93
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94 @HELP@
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95 ]]></help>
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96 <expand macro="citation"/>
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97 </tool>