Mercurial > repos > gga > apollo_fetch_jbrowse

annotate fetch_organism_jbrowse.xml @ 3:20c6db7856c6 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
author gga
date Wed, 20 Sep 2017 09:44:15 -0400
parents c6d7f19953a6
children 9968eec7430e
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1 <?xml version="1.0"?>
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2 <tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.2" 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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13
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14 python $__tool_directory__/fetch_organism_jbrowse.py
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15 @ADMIN_AUTH@
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16
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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 cp $dummyIndex $jbrowse &&
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21 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
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22 echo '</ul></body></html>' >> $jbrowse
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23
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24 ]]></command>
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25 <configfiles>
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26 <configfile name="dummyIndex">
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27 <![CDATA[
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28 <html>
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29 <head>
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30 </head>
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31 <body>
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32 <h1>JBrowse Data Directory</h1>
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33 <p>
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34 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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35 started shipping with the ability to produce just the
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36 "data" directory from a JBrowse instance, rather than a
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37 complete, standalone instance. This was intended to be used
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38 with the in-development Apollo integration, but may have other
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39 uses as well.
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40 </p>
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41 <p>
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42 <u>This is not usable on its own</u>. The output dataset may be
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43 used with Apollo, or may be passed through the "JBrowse -
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44 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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45 JBrowse instance.
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46 </p>
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47 <p>
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48 The following list is provided for your convenience / debugging.
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49 </p>
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50 <h2>Contained Files</h2>
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51 <ul>
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52 ]]>
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53 </configfile>
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54 </configfiles>
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55 <inputs>
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56 <expand macro="org_or_guess" />
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57 </inputs>
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58 <outputs>
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59 <data format="html" name="jbrowse"/>
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60 </outputs>
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61 <tests>
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62 <test expect_failure="true">
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63 <conditional name="org_source">
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64 <param name="source_select" value="direct"/>
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65 <param name="org_raw" value="Test org" />
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66 </conditional>
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67 <expand macro="test_result" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 **What it does**
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72
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73 Fetches the JBrowse directory from Apollo back into Galaxy.
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74
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75 .. class:: warningmark
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76
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77 If you provide an Apollo JSON file, only the first organism block will be used
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78 in Common Name determination, as it is improbable you wish to apply a single
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79 JBrowse instance to multiple organisms.
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80
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81 @REFERENCES@
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82 ]]></help>
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83 <expand macro="citations"/>
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84 </tool>