Mercurial > repos > devteam > data_manager_bowtie2_index_builder

annotate data_manager_conf.xml @ 2:8de13c28d92e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 10:17:27 -0400
parents eec64de5f7fb
children 49331eedb1c5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
2 <data_managers>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
3
2
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
4 <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder" version="0.0.2">
0
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
5 <data_table name="bowtie2_indexes">
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
6 <output>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
7 <column name="value" />
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
8 <column name="dbkey" />
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
9 <column name="name" />
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
10 <column name="path" output_ref="out_file" >
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
11 <move type="directory" relativize_symlinks="True">
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
12 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
13 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bowtie2_index/${value}</target>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
14 </move>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
15 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
16 <value_translation type="function">abspath</value_translation>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
17 </column>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
18 </output>
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
19 </data_table>
2
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
20
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
21 <data_table name="tophat2_indexes">
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
22 <output>
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
23 <column name="value" />
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
24 <column name="dbkey" />
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
25 <column name="name" />
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
26 <column name="path" output_ref="out_file" >
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
27 <!-- no move, always happens as part of bowtie2 and uses that path -->
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
28 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation>
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
29 <value_translation type="function">abspath</value_translation>
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
30 </column>
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
31 </output>
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
32 </data_table>
0
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
33 </data_manager>
2
8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
34
0
eec64de5f7fb Uploaded
devteam
parents:
diff changeset
35 </data_managers>