Mercurial > repos > devteam > emboss_5
annotate emboss_dan.xml @ 20:21a9fb508031 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:05:39 +0000 |
| parents | 27c43fb015f0 |
| children |
| rev | line source |
|---|---|
|
14
27c43fb015f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
parents:
11
diff
changeset
|
1 <tool id="EMBOSS: dan19" name="dan" version="@VERSION@.1"> |
|
11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
2 <description>Calculates DNA RNA/DNA melting temperature</description> |
|
20
21a9fb508031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
14
diff
changeset
|
3 <expand macro="bio_tools" /> |
|
11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
4 <macros> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
5 <import>macros.xml</import> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
6 </macros> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
7 <expand macro="requirements" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
8 <code file="emboss_format_corrector.py" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
9 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$input1' -windowsize $window -goutfile '$out_file1' -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
10 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
11 <inputs> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
12 <param name="input1" type="data" format="data" label="On query" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
13 <param name="window" type="integer" value="20" label="Window size" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
14 <param name="shift" type="integer" value="1" label="Step size (shift increment)" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
15 <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
16 <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
17 <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values"> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
18 <option value="yes">Yes</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
19 <option value="no">No</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
20 </param> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
21 <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
22 <param name="rna" type="select" label="Sequence is RNA"> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
23 <option value="no">No</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
24 <option value="yes">Yes</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
25 </param> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
26 <param name="product" type="select" label="Include percent formamide, percent of mismatches allowed and product length"> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
27 <option value="no">No</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
28 <option value="yes">Yes</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
29 </param> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
30 <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
31 <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
32 <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
33 <param name="plot1" type="select" label="Create a graph"> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
34 <option value="no">No</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
35 <option value="yes">Yes</option> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
36 </param> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
37 </inputs> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
38 <outputs> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
39 <data name="out_file1" format="dan" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
40 </outputs> |
|
10
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
41 <!-- |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
42 <tests> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
43 <test> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
44 <param name="input1" value="2.fasta"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
45 <param name="window" value="20"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
46 <param name="shift" value="1"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
47 <param name="dnaconc" value="50"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
48 <param name="saltconc" value="50"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
49 <param name="thermo" value="yes"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
50 <param name="temperature" value="25"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
51 <param name="rna" value="no"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
52 <param name="product" value="no"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
53 <param name="formamide" value="0"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
54 <param name="mismatch" value="0"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
55 <param name="prodlen" value="20"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
56 <param name="plot1" value="yes"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
57 <output name="out_file1" file="emboss_dan_out.png"/> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
58 </test> |
|
11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
59 </tests> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
60 --> |
|
10
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
61 <help> |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
62 You can view the original documentation here_. |
|
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
63 |
|
11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
64 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html |
|
10
9b98d3d903c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
diff
changeset
|
65 </help> |
|
11
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
66 <expand macro="citations" /> |
|
0e2484b6829b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents:
10
diff
changeset
|
67 </tool> |