Mercurial > repos > gga > apollo_fetch_jbrowse

comparison fetch_organism_jbrowse.xml @ 10:dca2fb399ee6 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:45:36 -0500
parents d8bb1f9b85b2
children d91f4bc313d3
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9:d8bb1f9b85b2 10:dca2fb399ee6
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="webapollo.py"/> 8 <code file="webapollo.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 mkdir -p $jbrowse.files_path/ 10 mkdir -p '$jbrowse.files_path/'
11 11
12 && 12 &&
13 13
14 python $__tool_directory__/fetch_organism_jbrowse.py 14 @AUTH@
15 @ADMIN_AUTH@ 15
16 python '$__tool_directory__/fetch_organism_jbrowse.py'
16 17
17 @ORG_OR_GUESS@ 18 @ORG_OR_GUESS@
18 $jbrowse.files_path/ 19 '$jbrowse.files_path/'
19 20
20 "$__user_email__" && 21 '$__user_email__' &&
21 22
22 cp $dummyIndex $jbrowse && 23 cp '$dummyIndex' '$jbrowse' &&
23 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse && 24 find '$jbrowse.files_path' -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
24 echo '</ul></body></html>' >> $jbrowse 25 echo '</ul></body></html>' >> '$jbrowse'
25 26
26 ]]></command> 27 ]]></command>
27 <configfiles> 28 <configfiles>
28 <configfile name="dummyIndex"> 29 <configfile name="dummyIndex">
29 <![CDATA[ 30 <![CDATA[
61 <data format="html" name="jbrowse"> 62 <data format="html" name="jbrowse">
62 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 63 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
63 </data> 64 </data>
64 </outputs> 65 </outputs>
65 <tests> 66 <tests>
66 <test expect_failure="true"> 67 <test>
67 <conditional name="org_source"> 68 <conditional name="org_source">
68 <param name="source_select" value="direct"/> 69 <param name="source_select" value="direct"/>
69 <param name="org_raw" value="Test org" /> 70 <param name="org_raw" value="alt_org" />
70 </conditional> 71 </conditional>
71 <expand macro="test_result" /> 72 <output name="jbrowse">
73 <assert_contents>
74 <has_text text="This is not a full JBrowse instance" />
75 </assert_contents>
76 </output>
72 </test> 77 </test>
73 </tests> 78 </tests>
74 <help><![CDATA[ 79 <help><![CDATA[
75 **What it does** 80 **What it does**
76 81