Mercurial > repos > devteam > lastz
annotate lastz_macros.xml @ 5:bd84ff27bc16 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
author | devteam |
---|---|
date | Mon, 26 Feb 2018 15:37:53 -0500 |
parents | |
children | b6d7308c3728 |
rev | line source |
---|---|
5
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
1 <macros> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
2 <token name="@LASTZ_CONDA_VERSION@">1.0.4</token> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
3 <token name="@TARGET_INPUT_COMMAND_LINE@"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
4 #if $source.ref_source=="history": |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
5 '${source.target}' |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
6 #else: |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
7 '${source.target_2bit.fields.path}' |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
8 #end if |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
9 </token> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
10 <xml name="target_input"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
11 <conditional name="source"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
12 <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
13 <option value="cached">locally cached</option> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
14 <option value="history">from your history</option> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
15 </param> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
16 <when value="cached"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
17 <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
18 <options from_data_table="lastz_seqs" /> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
19 </param> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
20 </when> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
21 <when value="history"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
22 <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" /> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
23 </when> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
24 </conditional> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
25 </xml> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
26 <xml name="citations"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
27 <citations> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
28 <citation type="bibtex"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
29 @misc{ |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
30 githublastz, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
31 author = {Harris, Robert}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
32 year = {2007}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
33 title = {Improved pairwise alignment of genomic DNA}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
34 publisher = {The Pennsylvania State University}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
35 journal = {Ph. D. Thesis}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
36 url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
37 } |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
38 </citation> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
39 </citations> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
40 </xml> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
|
41 </macros> |