Mercurial > repos > gga > apollo_fetch_jbrowse
comparison fetch_organism_jbrowse.xml @ 10:dca2fb399ee6 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author | gga |
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date | Mon, 02 Dec 2019 05:45:36 -0500 |
parents | d8bb1f9b85b2 |
children | d91f4bc313d3 |
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9:d8bb1f9b85b2 | 10:dca2fb399ee6 |
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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<designation>.+)\.txt" format="tabular" visible="true"/> | 63 <discover_datasets pattern="(?P<designation>.+)\.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 |