Mercurial > repos > matthias > stacks2_denovomap
annotate macros.xml @ 3:33ca88a71f08 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
| author | matthias |
|---|---|
| date | Fri, 04 Jan 2019 03:33:53 -0500 |
| parents | fa593b13402f |
| children | a70c766ce64f |
| rev | line source |
|---|---|
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
2 <macros> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
3 <xml name="requirements"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
4 <requirements> |
|
1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
0
diff
changeset
|
5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
6 <yield/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
7 </requirements> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
8 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
9 |
|
1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
0
diff
changeset
|
10 <token name="@STACKS_VERSION@">2.2</token> |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
11 <token name="@WRAPPER_VERSION@">2</token> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
12 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
13 <xml name="stdio"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
14 <stdio> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
15 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
16 </stdio> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
17 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
18 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
19 <xml name="citation"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
20 <citations> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
21 <citation type="doi">10.1111/mec.12354</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
22 <citation type="doi">10.1111/mec.12330</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
23 <citation type="doi">10.1534/g3.111.000240</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
24 <citation type="doi">10.1534/genetics.111.127324</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
25 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
26 <citation type="doi">10.1073/pnas.1006538107</citation> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
27 </citations> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
28 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
29 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
30 <xml name="version_cmd"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
31 <version_command><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
32 process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
33 ]]> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
34 </version_command> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
35 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
36 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
37 <token name="@STACKS_INFOS@"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
38 <![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
39 -------- |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
40 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
41 **Created by:** |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
42 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
43 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
44 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
45 **Project links:** |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
46 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
47 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
48 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
49 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
50 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
51 `Stacks google group <http://groups.google.com/group/stacks-users>`_ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
52 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
53 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
54 <xml name="enzymes"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
55 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
56 <option value="">Unspecified</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
57 <option value="aciI">aciI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
58 <option value="ageI">ageI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
59 <option value="aluI">aluI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
60 <option value="apaLI">apaLI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
61 <option value="apeKI">apeKI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
62 <option value="apoI">apoI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
63 <option value="aseI">aseI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
64 <option value="bamHI">bamHI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
65 <option value="bbvCI">bbvCI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
66 <option value="bfaI">bfaI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
67 <option value="bfuCI">bfuCI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
68 <option value="bgIII">bgIII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
69 <option value="bsaHI">bsaHI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
70 <option value="bspDI">bspDI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
71 <option value="bstYI">bstYI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
72 <option value="cac8I">cac8I</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
73 <option value="claI">claI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
74 <option value="csp6I">csp6I</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
75 <option value="ddeI">ddeI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
76 <option value="dpnII">dpnII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
77 <option value="eaeI">eaeI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
78 <option value="ecoRI">ecoRI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
79 <option value="ecoRV">ecoRV</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
80 <option value="ecoT22I">ecoT22I</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
81 <option value="haeIII">haeIII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
82 <option value="hindIII">hindIII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
83 <option value="hinP1I">hinP1I</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
84 <option value="hpaII">hpaII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
85 <option value="kpnI">kpnI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
86 <option value="mluCI">mluCI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
87 <option value="mseI">mseI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
88 <option value="mslI">mslI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
89 <option value="mspI">mspI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
90 <option value="ncoI">ncoI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
91 <option value="ndeI">ndeI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
92 <option value="nheI">nheI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
93 <option value="nlaIII">nlaIII</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
94 <option value="notI">notI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
95 <option value="nsiI">nsiI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
96 <option value="nspI">nspI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
97 <option value="pstI">pstI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
98 <option value="rsaI">rsaI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
99 <option value="sacI">sacI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
100 <option value="sau3AI">sau3AI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
101 <option value="sbfI">sbfI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
102 <option value="sexAI">sexAI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
103 <option value="sgrAI">sgrAI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
104 <option value="speI">speI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
105 <option value="sphI">sphI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
106 <option value="taqI">taqI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
107 <option value="xbaI">xbaI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
108 <option value="xhoI">xhoI</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
109 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
110 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
111 <!-- log file handling --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
112 <token name="@TEE_APPEND_LOG@"><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
113 #if $output_log |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
114 2>> $output_log && |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
115 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
116 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
117 <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
118 #if $output_log |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
119 cat $output_log 2>&1 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
120 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
121 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
122 <xml name="in_log"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
123 <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as data set" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
124 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
125 <xml name="out_log"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
127 <filter>add_log</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
128 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
129 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
130 |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
131 <!-- inputs from previous pipeline steps --> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
132 <xml name="input_cat_macro"> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
133 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
134 </xml> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
135 <xml name="input_tags_macro"> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
136 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" /> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
137 </xml> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
138 <xml name="input_matches_macro"> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
139 <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" /> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
140 </xml> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
141 <xml name="input_aln_macro"> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
142 <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
143 </xml> |
|
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
144 |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
145 |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
146 <!-- fastq input --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
147 <xml name="fastq_input_macro" token_fastq_optional="false"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
148 <conditional name="input_type"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
149 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
150 <option value="manual" selected="true">single end or forward reads</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
151 <option value="list">(paired) data set list</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
152 </param> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
153 <when value="manual"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
154 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
155 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
156 <when value="list"> |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
157 <param name="samples" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
158 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
159 </conditional> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
160 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
161 <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
162 appends noting/.1/.2 to the link name for accessing the fastq data |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
163 sets variables $name and $data_path--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
164 <token name="@FASTQ_INPUT@"><![CDATA[ |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
165 ## TODO should use sample.identidfier if possible (see corresp. preproc macro) |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
166 #set $name = $clean_ext($sample.name) |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
167 #set $data_path = "stacks_inputs/" + $name |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
168 #if $sample.is_collection: |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
169 #set $cur_sample=$sample[$read_direction] |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
170 #else: |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
171 #set $cur_sample=$sample |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
172 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
173 #if $read_direction == "forward": |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
174 #set $data_path = $data_path + ".1" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
175 #elif $read_direction == "reverse": |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
176 #set $data_path = $data_path + ".2" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
177 #end if |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
178 #if $cur_sample.is_of_type('fastqsanger') |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
179 #set $data_path = $data_path + ".fq" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
180 #set inputype = "fastq" |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
181 #else if $cur_sample.is_of_type('fastqsanger.gz') |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
182 #set $data_path = $data_path + ".fq.gz" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
183 #set inputype = "gzfastq" |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
184 #else if $cur_sample.is_of_type('fasta') |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
185 #set $data_path = $data_path + ".fa" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
186 #set inputype = "fasta" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
187 #else |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
188 #set $data_path = $data_path + ".fa.gz" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
189 #set inputype = "gzfasta" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
190 #end if |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
191 ln -s '$cur_sample' '${data_path}' && |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
192 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
193 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
194 <!-- macro and token for BAM input--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
195 <xml name="bam_input_macro"> |
|
1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
0
diff
changeset
|
196 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" /> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
197 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
198 <token name="@BAM_INPUT@"><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
199 #set $bamlist = "" |
|
1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
parents:
0
diff
changeset
|
200 #for $bam in $input_bam: |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
201 #set $filename = $clean_ext($bam.element_identifier)+".bam" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
202 #if re.search('.*\.bam$', $filename) |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
203 ln -s '$bam' bam_inputs/$filename && |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
204 #set bamlist += " -B 'bam_inputs/"+$filename+"'" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
205 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
206 #end for |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
207 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
208 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
209 <token name="@CLEAN_EXT@"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
210 <![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
211 #from os.path import splitext |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
212 #import re |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
213 #def clean_ext($identifier) |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
214 #while $identifier.endswith(('.1', '.2', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
215 #set $identifier = splitext($identifier)[0] |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
216 #end while |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
217 $identifier#slurp |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
218 #end def |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
219 ]]> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
220 </token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
221 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
222 <!-- tokens and macros for gapped alignment options |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
223 the _onoff macro gives an empty conditional (which is not so nice |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
224 but allows to be used also in the full macro) --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
225 <token name="@GAP_OPTIONS@"><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
226 #if $gapped.use_gapped == "yes" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
227 --max_gaps $gapped.max_gaps |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
228 --min_aln_len $gapped.min_aln_len |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
229 #else |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
230 --disable-gapped |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
231 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
232 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
233 <token name="@GAP_OPTIONS_ONOFF@"><![CDATA[ |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
234 #if $gapped.use_gapped != "yes" |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
235 --disable-gapped |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
236 #end if |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
237 ]]></token> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
238 <xml name="gap_options"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
239 <expand macro="gap_options_onoff"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
240 <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
241 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
242 </expand> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
243 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
244 <xml name="gap_options_onoff"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
245 <conditional name="gapped"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
246 <param name="use_gapped" argument="--disable-gapped" type="select" label="Perform gapped alignments between stacks"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
247 <option value="no">No</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
248 <option value="yes" selected="true">Yes</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
249 </param> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
250 <when value="no"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
251 <when value="yes"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
252 <yield/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
253 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
254 </conditional> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
255 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
256 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
257 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
258 <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
259 <xml name="ustacks_outputs_macro" token_tooladd=""> |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
260 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci per sample"> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
261 <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
262 <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
263 <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
264 </collection> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
265 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
266 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
267 <xml name="cstacks_outputs_macro" token_tooladd=""> |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
268 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci"> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
269 <discover_datasets pattern="(?P<name>catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
270 </collection> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
271 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
272 <!-- sstacks outputs collection containing SAMPLE.matches.tsv --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
273 <xml name="sstacks_outputs_macro" token_tooladd=""> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
274 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
275 <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
276 </collection> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
277 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
278 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
279 <xml name="tsv2bam_outputs_macro" token_tooladd=""> |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
280 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci"> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
281 <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
282 </collection> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
283 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
284 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
285 <xml name="gstacks_outputs_macro" token_tooladd=""> |
|
3
33ca88a71f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
matthias
parents:
2
diff
changeset
|
286 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites"> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
287 <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
288 <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
289 </collection> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
290 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
291 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
292 <!-- default output of populations --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
293 <xml name="populations_output_light" token_tooladd=""> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
294 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
295 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
296 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
297 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
298 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
299 <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
300 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
301 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
302 <xml name="populations_output_full"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
303 <expand macro="populations_output_light"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
304 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
305 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
306 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
307 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
308 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
309 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
310 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
311 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
312 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
313 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
314 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
315 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
316 <!-- fasta_loci populations.loci.fa |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
317 fasta_samples populations.samples.fa |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
318 fasta_samples_raw populations.samples-raw.fa--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
319 <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
320 <filter>populations_output['fasta_loci']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
321 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
322 <data format="tabular" name="out_fasta" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences" from_work_dir="stacks_outputs/populations.samples.fa"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
323 <filter>populations_output['fasta_samples']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
324 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
325 <data format="tabular" name="out_fasta_raw" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences (regardless of biological plausibility)" from_work_dir="stacks_outputs/populations.samples-raw.fa"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
326 <filter>populations_output['fasta_samples_raw']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
327 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
328 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
329 <!-- phylip populations.fixed.phylip populations.fixed.phylip.log |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
330 phylip_var populations.var.phylip populations.var.phylip.log--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
331 <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
332 <filter>populations_output['phylip']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
333 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
334 <data format="tabular" name="out_phylip_all_loci_fix" label="${tool.name} on ${on_string} Phylip (loci) nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip.log"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
335 <filter>populations_output['phylip']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
336 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
337 <data format="tabular" name="out_phylip_all_pop_var" label="${tool.name} on ${on_string} Phylip all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
338 <filter>populations_output['phylip_var']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
339 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
340 <data format="tabular" name="out_phylip_all_loci_var" label="${tool.name} on ${on_string} Phylip (loci) all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip.log"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
341 <filter>populations_output['phylip_var']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
342 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
343 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
344 <!-- genepop populations.haps.genepop populations.snps.genepop --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
345 <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
346 <filter>populations_output['genepop']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
347 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
348 <data format="tabular" name="out_genepop_haps" label="${tool.name} on ${on_string} Haplotypes in GenePop format" from_work_dir="stacks_outputs/populations.haps.genepop"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
349 <filter>populations_output['genepop']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
350 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
351 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
352 <!-- vcf populations.haps.vcf populations.snps.vcf --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
353 <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
354 <filter>populations_output['vcf']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
355 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
356 <data format="vcf" name="out_vcf_haplotypes_haps" label="${tool.name} on ${on_string} Haplotypes in VCF format" from_work_dir="stacks_outputs/populations.haps.vcf"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
357 <filter>populations_output['vcf']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
358 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
359 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
360 <!--plink populations.plink.map populations.plink.ped--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
361 <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
362 <filter>populations_output['plink']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
363 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
364 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
365 <filter>populations_output['plink']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
366 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
367 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
368 <!--structure populations.structure--> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
369 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
370 <filter>populations_output['structure']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
371 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
372 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
373 <!-- radpainter populations.haps.radpainter --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
374 <data format="tabular" name="out_radpainter" label="${tool.name} on ${on_string} Radpainter format" from_work_dir="stacks_outputs/populations.haps.radpainter"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
375 <filter>populations_output['radpainter']</filter> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
376 </data> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
377 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
378 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
379 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
380 <xml name="snp_options_alpha"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
381 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
382 <option value="0.1">0.1</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
383 <option value="0.05" selected="True">0.05</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
384 <option value="0.01">0.01</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
385 <option value="0.001">0.001</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
386 </param> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
387 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
388 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
389 <xml name="snp_options"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
390 <conditional name="select_model"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
391 <param argument="--model_type" type="select" label="Choose the model"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
392 <option value="snp" selected="true">SNP</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
393 <option value="bounded">Bounded SNP</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
394 <option value="fixed">Fixed</option> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
395 </param> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
396 <when value="snp"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
397 <expand macro="snp_options_alpha"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
398 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
399 <when value="bounded"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
400 <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
401 <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
402 <expand macro="snp_options_alpha"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
403 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
404 <when value="fixed"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
405 <yield/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
406 </when> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
407 </conditional> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
408 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
409 <xml name="snp_options_full"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
410 <expand macro="snp_options"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
411 <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
412 </expand> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
413 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
414 |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
415 <!-- variant calling option for use in gstacks and denovomap --> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
416 <xml name="variant_calling_options_vg"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
417 <param argument="--var-alpha" name="var_alpha" type="float" value="0.05" min="0" label="alpha threshold for discovering SNPs" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
418 <expand macro="variant_calling_options_g"/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
419 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
420 <xml name="variant_calling_options_g"> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
421 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" /> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
422 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
423 |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
424 <xml name="barcode_encoding_single" token_type=""> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
425 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
426 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
427 <yield/> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
428 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
429 |
|
2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
430 <xml name="barcode_encoding_pair" token_type=""> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
431 <expand macro="barcode_encoding_single" type="@TYPE@"> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
432 <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
433 <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
434 <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
435 <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option> |
|
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
parents:
1
diff
changeset
|
436 <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option> |
|
0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
437 </expand> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
438 </xml> |
|
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
changeset
|
439 </macros> |