annotate jbrowse-fromdir.xml @ 25:1cfc579079a6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
author iuc
date Tue, 29 Jan 2019 05:34:16 -0500
parents 5f70e7fe6077
children 3235aeb45c22
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
2 <description>upgrades the bare data directory to a full JBrowse instance</description>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
3 <macros>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
4 <import>macros.xml</import>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
5 </macros>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 22
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
8 ## Create output directory
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
9 mkdir -p $output.files_path &&
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
10 ## Copy in jbrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
11 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
12
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
13 ## Copy in data directory
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
14 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
15 mv $output.files_path/index.html $output
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
16 ]]></command>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
17 <inputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
18 <param label="JBrowse Data Directory"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
19 name="input"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
20 type="data"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
21 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
22 format="html" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
23 </inputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
24 <outputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
25 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
26 </outputs>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
27 <tests>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
28 </tests>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
29 <help><![CDATA[
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
30 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
31
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
32 @ATTRIBUTION@
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
33 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
34 <expand macro="citations"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
35 </tool>