Mercurial > repos > gga > apollo_fetch_jbrowse

annotate fetch_organism_jbrowse.xml @ 5:1a2976c6b161 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author gga
date Fri, 31 Aug 2018 09:33:16 -0400
parents 9968eec7430e
children d8bb1f9b85b2
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1 <?xml version="1.0"?>
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2 <tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.3" 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 <code file="webapollo.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 mkdir -p $jbrowse.files_path/
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11
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12 &&
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14 python $__tool_directory__/fetch_organism_jbrowse.py
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15 @ADMIN_AUTH@
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17 @ORG_OR_GUESS@
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18 $jbrowse.files_path/
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19
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20 "$__user_email__" &&
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22 cp $dummyIndex $jbrowse &&
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23 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
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24 echo '</ul></body></html>' >> $jbrowse
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25
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26 ]]></command>
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27 <configfiles>
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28 <configfile name="dummyIndex">
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29 <![CDATA[
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30 <html>
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31 <head>
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32 </head>
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33 <body>
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34 <h1>JBrowse Data Directory</h1>
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35 <p>
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36 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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37 started shipping with the ability to produce just the
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38 "data" directory from a JBrowse instance, rather than a
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39 complete, standalone instance. This was intended to be used
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40 with the in-development Apollo integration, but may have other
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41 uses as well.
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42 </p>
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43 <p>
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44 <u>This is not usable on its own</u>. The output dataset may be
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45 used with Apollo, or may be passed through the "JBrowse -
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46 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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47 JBrowse instance.
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48 </p>
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49 <p>
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50 The following list is provided for your convenience / debugging.
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51 </p>
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52 <h2>Contained Files</h2>
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53 <ul>
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54 ]]>
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55 </configfile>
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56 </configfiles>
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57 <inputs>
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58 <expand macro="org_or_guess" />
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59 </inputs>
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60 <outputs>
5
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61 <data format="html" name="jbrowse">
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62 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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63 </data>
0
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64 </outputs>
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65 <tests>
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66 <test expect_failure="true">
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67 <conditional name="org_source">
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68 <param name="source_select" value="direct"/>
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69 <param name="org_raw" value="Test org" />
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70 </conditional>
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71 <expand macro="test_result" />
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 **What it does**
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76
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77 Fetches the JBrowse directory from Apollo back into Galaxy.
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78
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79 .. class:: warningmark
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80
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81 If you provide an Apollo JSON file, only the first organism block will be used
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82 in Common Name determination, as it is improbable you wish to apply a single
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83 JBrowse instance to multiple organisms.
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84
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85 @REFERENCES@
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86 ]]></help>
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87 <expand macro="citations"/>
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88 </tool>