Mercurial > repos > guerler > ffindex_dbkit_extract

annotate dbkit_extract.xml @ 3:4def47766a3c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:20:04 +0000
parents 1d9fcf2157e0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1d9fcf2157e0 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
1 <tool id="ffindex_dbkit_extract" name="DBKit Extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
0
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
2 <description>entries</description>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
3 <macros>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
4 <import>macros.xml</import>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
5 </macros>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
6 <expand macro="requirements" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
8 dbkit_extract.py
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
9 -l '$list'
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
10 @db_source@
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
11 -oi '$outindex'
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
12 -od '$outdata'
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
13 -g '$logfile'
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
14 ]]> </command>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
15 <inputs>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
16 <param name="list" type="data" format="tabular" label="List of entries" help="Select a tabular file containing the entries to be extracted." />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
17 <expand macro="db_source" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
18 <expand macro="logfile" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
19 </inputs>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
20 <outputs>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
21 <data format="ffindex" name="outindex" label="DBKit Extracted Index" />
3
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
22 <data format="ffdata" name="outdata" label="DBKit Extracted Database" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
23 <data format="txt" name="logfile" label="DBKit Extracted Log">
0
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
24 <filter>logfile</filter>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
25 </data>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
26 </outputs>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
27 <tests>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
28 <test>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
29 <param name="list" value="create/pdb.tabular" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
30 <conditional name="db_source">
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
31 <param name="db_source_selector" value="history" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
32 <param name="ffindex" value="merge/result.ffindex" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
33 <param name="ffdata" value="merge/result.ffdata" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
34 </conditional>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
35 <output name="outindex" file="merge/second.ffindex" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
36 <output name="outdata" file="merge/second.ffdata" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
37 </test>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
38 <test>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
39 <param name="list" value="create/pdb.tabular" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
40 <conditional name="db_source">
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
41 <param name="db_source_selector" value="indexed" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
42 <param name="ffindex" value="merge" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
43 </conditional>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
44 <output name="outindex" file="merge/second.ffindex" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
45 <output name="outdata" file="merge/second.ffdata" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
46 </test>
3
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
47 <test>
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
48 <param name="list" value="create/pdb_gz.tabular" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
49 <conditional name="db_source">
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
50 <param name="db_source_selector" value="indexed" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
51 <param name="ffindex" value="first_gz" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
52 </conditional>
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
53 <output name="outindex" file="extract/third.ffindex" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
54 <output name="outdata" file="extract/third.ffdata" />
4def47766a3c "planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
guerler
parents: 1
diff changeset
55 </test>
0
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
56 </tests>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
57 <help><![CDATA[
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
58
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
59 **What it does**
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
60
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
61 This database creation tool merges two pairs of ffindex/ffdata entries into a single ffindex/ffdata pair.
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
62 ]]> </help>
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
63 <expand macro="citations" />
ad4b7db26523 "planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
guerler
parents:
diff changeset
64 </tool>