Mercurial > repos > gga > tripal_analysis_load_interpro

annotate analysis_load_interpro.xml @ 2:e784e9a1cda9 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:38:51 -0400
parents dc0a6c9cea1c
children 1e2fcb5c8bd2
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1 <?xml version="1.0"?>
2
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2 <tool id="analysis_load_interpro" profile="16.04" name="Load InterProScan results" version="@WRAPPER_VERSION@.1">
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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 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
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12 &&
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14 cp '${input}' "\${tmp_dir}/interpro.xml"
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16 &&
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18 @AUTH@
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20 tripaille analysis load_interpro
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22 @ANALYSIS@
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24 --interpro_parameters '${params}'
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26 ${parse_go}
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28 @MATCHING@
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29
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30 "\${tmp_dir}/interpro.xml"
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32 &&
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33
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34 echo "Data loaded" > $results
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35 ]]></command>
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36 <inputs>
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37 <param name="input"
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38 type="data"
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39 format="xml"
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40 label="InterProScan results" />
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41
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42 <param name="parse_go"
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43 type="boolean"
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44 checked="true"
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45 truevalue="--parse_go"
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46 falsevalue=""
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47 label="Load GO annotation to the database" />
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48
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49 <param name="params"
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50 type="text"
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51 label="InterProScan parameters used to produce the results" />
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52
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53 <expand macro="matching"/>
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54 <expand macro="analysis" />
2
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55 <expand macro="wait_for"/>
0
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56 </inputs>
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57 <outputs>
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58 <data format="txt" name="results" label="Load InterProScan results into Tripal" />
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59 </outputs>
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60 <tests>
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61 <test expect_failure="true" expect_exit_code="1">
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62 <param name="input" value="interpro.xml" />
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63 <param name="parse_go" value="true" />
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64 <param name="params" value="--some --param" />
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65 <param name="query_type" value="mRNA" />
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66 <param name="query_uniquename" value="true" />
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67 <section name="analysis">
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68 <param name="name" value="Some analysis" />
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69 <param name="program" value="interproscan" />
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70 <param name="program_version" value="58.2" />
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71 <param name="algorithm" value="interproscan" />
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72 <param name="source" value="NCBI" />
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73 <param name="source_version" value="1.0" />
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74 <param name="source_uri" value="http://ncbi.com/somewhere" />
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75 <param name="description" value="My cool new test analysis" />
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76 <param name="date" value="2016-12-12" />
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77 </section>
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78
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79 <expand macro="test_result" />
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 @HELP_OVERVIEW@
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84
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85 **Load InterProScan results**
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86
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87 With this tool, you can load InterProScan results into the Tripal/Chado database.
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88
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89 A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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90
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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91 The `tripal_analysis_interpro <http://github.com/tripal/tripal_analysis_interpro>`_ module must be installed and configured on the Tripal instance.
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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92
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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93 @HELP@
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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94 ]]></help>
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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95 <expand macro="citation"/>
dc0a6c9cea1c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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96 </tool>