Mercurial > repos > gga > tripal_analysis_load_blast

annotate analysis_load_blast.xml @ 5:d07a4cbb951b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 35c5eff77b573a66f3611b4906417df9a440c857
author gga
date Tue, 05 Mar 2019 05:20:55 -0500
parents bd4d410ac108
children
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1 <?xml version="1.0"?>
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2 <tool id="analysis_load_blast" profile="16.04" name="Load Blast 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 '${blast_output}' "\${tmp_dir}/blast_input.xml"
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17 &&
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19 @AUTH@
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21 tripaille analysis load_blast
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23 --is_concat
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25 --blastdb_id '${blastdb}'
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27 --blast_parameters '${params}'
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29 @MATCHING@
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31 @ANALYSIS@
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33 "\${tmp_dir}/blast_input.xml"
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34
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35 &&
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36
5
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37 echo "Data loaded" > '$results'
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38 ]]></command>
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39 <inputs>
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40 <param name="blast_output"
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41 type="data"
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42 format="xml"
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43 label="Blast blast_output" />
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45 <param argument="--blastdb"
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46 type="select"
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47 dynamic_options="list_blastdbs()"
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48 label="Blast databank used" />
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49
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50 <param name="params"
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51 type="text"
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52 label="Blast parameters used to produce the results" />
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53
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54 <expand macro="matching"/>
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55
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56 <expand macro="analysis" />
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57 <expand macro="wait_for"/>
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58 </inputs>
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59 <outputs>
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60 <data format="txt" name="results" label="Load Blast results into Tripal" />
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61 </outputs>
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62 <tests>
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63 <test expect_failure="true" expect_exit_code="1">
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64 <param name="blast_output" value="blast.xml" />
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65 <param name="blastdb" value="genbank:protein" />
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66 <param name="params" value="-e 0.001" />
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67 <param name="query_type" value="mRNA" />
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68 <param name="query_uniquename" value="true" />
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69 <section name="analysis">
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70 <param name="name" value="Some analysis" />
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71 <param name="program" value="blastp" />
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72 <param name="program_version" value="2.5.0" />
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73 <param name="algorithm" value="blast" />
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74 <param name="source" value="NCBI" />
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75 <param name="source_version" value="1.0" />
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76 <param name="source_uri" value="http://ncbi.com/somewhere" />
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77 <param name="description" value="My cool new test analysis" />
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78 <param name="date" value="2016-12-12" />
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79 </section>
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81 <expand macro="test_result" />
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 @HELP_OVERVIEW@
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86
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87 **Load Blast results**
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88
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89 With this tool, you can load Blast results into the Tripal/Chado database.
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90
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91 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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92
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93 The `tripal_analysis_blast <http://github.com/tripal/tripal_analysis_blast>`_ module must be installed and configured on the Tripal instance.
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94
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95 @HELP@
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96 ]]></help>
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97 <expand macro="citation"/>
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98 </tool>