Mercurial > repos > iuc > jbrowse

annotate jbrowse-fromdir.xml @ 45:a6e57ff585c0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 80fbf6800feb0bb02c047d37e97b7a12e9c68f4c"
author iuc
date Fri, 23 Apr 2021 11:37:36 +0000
parents 8774b28235bb
children
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>
41
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
6 <edam_operations>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
7 <edam_operation>operation_3434</edam_operation>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
8 </edam_operations>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
9 <edam_topics>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
10 <edam_topic>topic_3307</edam_topic>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
11 <edam_topic>topic_0092</edam_topic>
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents: 35
diff changeset
12 </edam_topics>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
13 <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
14 <command detect_errors="exit_code"><![CDATA[
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
15 ## Create output directory
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
16 mkdir -p $output.files_path &&
35
3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
iuc
parents: 25
diff changeset
17
3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
iuc
parents: 25
diff changeset
18 export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse &&
3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
iuc
parents: 25
diff changeset
19
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
20 ## Copy in jbrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
21 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
22
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
23 ## Copy in data directory
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
24 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
35
3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
iuc
parents: 25
diff changeset
25 cp $output.files_path/index.html $output
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
26 ]]></command>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
27 <inputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
28 <param label="JBrowse Data Directory"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
29 name="input"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
30 type="data"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
31 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
32 format="html" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
33 </inputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
34 <outputs>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
35 <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
36 </outputs>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
37 <tests>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
38 </tests>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
39 <help><![CDATA[
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
40 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
41
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
42 @ATTRIBUTION@
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
43 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 3
diff changeset
44 <expand macro="citations"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
45 </tool>