annotate analysis_load_go.xml @ 0:81f5e6980725 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:51:44 -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 <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}/blast2go.gaf"
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16 &&
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18 @AUTH@
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20 tripaille analysis load_go
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22 @ANALYSIS@
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24 @MATCHING@
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25
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26 "\${tmp_dir}/blast2go.gaf"
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27
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28 &&
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30 echo "Data loaded" > $results
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31 ]]></command>
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32 <inputs>
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33 <param name="input"
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34 type="data"
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35 format="txt"
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36 label="Blast2Go results (GAF file)" />
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37
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38 <expand macro="matching"/>
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39 <expand macro="analysis" />
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40 </inputs>
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41 <outputs>
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42 <data format="txt" name="results" label="Load Blast2GO results into Tripal" />
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43 </outputs>
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44 <tests>
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45 <test expect_failure="true" expect_exit_code="1">
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46 <param name="input" value="blast2go.gaf" />
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47 <param name="query_type" value="polypeptide" />
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48 <param name="query_uniquename" value="true" />
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49 <section name="analysis">
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50 <param name="name" value="Some analysis" />
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51 <param name="program" value="interproscan" />
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52 <param name="program_version" value="58.2" />
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53 <param name="algorithm" value="blast2go" />
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54 <param name="source" value="NCBI" />
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55 <param name="source_version" value="1.0" />
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56 <param name="source_uri" value="http://ncbi.com/somewhere" />
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57 <param name="description" value="My cool new test analysis" />
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58 <param name="date" value="2016-12-12" />
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59 </section>
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60
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61 <expand macro="test_result" />
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 @HELP_OVERVIEW@
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66
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67 **Load Blast2Go results**
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68
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69 With this tool, you can load Blast2go results into the Tripal/Chado database.
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70
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71 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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72
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73 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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74
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75 @HELP@
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76 ]]></help>
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77 <expand macro="citation"/>
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78 </tool>