Mercurial > repos > gga > apollo_fetch_jbrowse

annotate fetch_organism_jbrowse.xml @ 17:d91f4bc313d3 draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author gga
date Wed, 11 Jan 2023 11:48:24 +0000
parents dca2fb399ee6
children
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1 <?xml version="1.0"?>
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2 <tool id="fetch_jbrowse" name="Retrieve JBrowse" version="@WRAPPER_VERSION@" profile="16.04">
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3 <description>for an organism, from Apollo</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 <requirement type="package" version="3.2.7">rsync</requirement>
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9 </expand>
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10 <code file="webapollo.py"/>
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11 <command detect_errors="aggressive"><![CDATA[
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12 mkdir -p '$jbrowse.files_path/'
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14 &&
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16 @AUTH@
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18 python '$__tool_directory__/fetch_organism_jbrowse.py'
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20 @ORG_OR_GUESS@
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21 '$jbrowse.files_path/'
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22
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23 '$__user_email__' &&
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24
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25 cp '$dummyIndex' '$jbrowse' &&
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26 find '$jbrowse.files_path' -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
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27 echo '</ul></body></html>' >> '$jbrowse'
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28
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29 ]]></command>
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30 <configfiles>
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31 <configfile name="dummyIndex">
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32 <![CDATA[
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33 <html>
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34 <head>
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35 </head>
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36 <body>
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37 <h1>JBrowse Data Directory</h1>
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38 <p>
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39 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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40 started shipping with the ability to produce just the
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41 "data" directory from a JBrowse instance, rather than a
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42 complete, standalone instance. This was intended to be used
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43 with the in-development Apollo integration, but may have other
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44 uses as well.
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45 </p>
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46 <p>
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47 <u>This is not usable on its own</u>. The output dataset may be
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48 used with Apollo, or may be passed through the "JBrowse -
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49 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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50 JBrowse instance.
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51 </p>
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52 <p>
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53 The following list is provided for your convenience / debugging.
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54 </p>
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55 <h2>Contained Files</h2>
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56 <ul>
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57 ]]>
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58 </configfile>
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59 </configfiles>
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60 <inputs>
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61 <expand macro="org_or_guess" />
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62 </inputs>
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63 <outputs>
5
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64 <data format="html" name="jbrowse">
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65 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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66 </data>
0
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67 </outputs>
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68 <tests>
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69 <test>
0
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70 <conditional name="org_source">
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71 <param name="source_select" value="direct"/>
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72 <param name="org_raw" value="alt_org" />
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73 </conditional>
10
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74 <output name="jbrowse">
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75 <assert_contents>
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76 <has_text text="This is not a full JBrowse instance" />
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77 </assert_contents>
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78 </output>
0
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 **What it does**
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83
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84 Fetches the JBrowse directory from Apollo back into Galaxy.
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85
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86 .. class:: warningmark
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87
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88 If you provide an Apollo JSON file, only the first organism block will be used
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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89 in Common Name determination, as it is improbable you wish to apply a single
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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90 JBrowse instance to multiple organisms.
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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91
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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92 @REFERENCES@
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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93 ]]></help>
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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94 <expand macro="citations"/>
c6d7f19953a6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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95 </tool>