Mercurial > repos > rnateam > selectsequencesfrommsa
annotate selectsequencesfrommsa.xml @ 1:876c70c6ecad draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit 3f736a6e9040a880a887c89271c9a8d5ac4c0c83-dirty
| author | rnateam |
|---|---|
| date | Fri, 08 Feb 2019 14:53:45 -0500 |
| parents | 48fc2c21fe1c |
| children |
| rev | line source |
|---|---|
|
1
876c70c6ecad
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit 3f736a6e9040a880a887c89271c9a8d5ac4c0c83-dirty
rnateam
parents:
0
diff
changeset
|
1 <tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.5"> |
|
0
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
2 <description> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
3 Tool to select representative sequences from a multiple sequence alignment. |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
4 </description> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
5 <requirements> |
|
1
876c70c6ecad
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit 3f736a6e9040a880a887c89271c9a8d5ac4c0c83-dirty
rnateam
parents:
0
diff
changeset
|
6 <requirement type="package" version="1.0.5">selectsequencesfrommsa</requirement> |
|
0
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
7 </requirements> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
8 <command detect_errors="aggressive"><![CDATA[ |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
9 SelectSequencesFromMSA |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
10 -c '$input_clustal' |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
11 $x |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
12 -o `pwd` |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
13 -n $n |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
14 -i $i |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
15 -m $m |
|
1
876c70c6ecad
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit 3f736a6e9040a880a887c89271c9a8d5ac4c0c83-dirty
rnateam
parents:
0
diff
changeset
|
16 -f result.selected |
|
0
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
17 > warnings |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
18 ]]> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
19 </command> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
20 <inputs> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
21 <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
22 <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
23 <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
24 <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
25 <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
26 </inputs> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
27 <outputs> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
28 <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
29 </outputs> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
30 <tests> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
31 <test> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
32 <param name="input_clustal" value="result.clustal"/> |
|
1
876c70c6ecad
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit 3f736a6e9040a880a887c89271c9a8d5ac4c0c83-dirty
rnateam
parents:
0
diff
changeset
|
33 <output name="clustal" file="result.selected"/> |
|
0
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
34 </test> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
35 </tests> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
36 <help> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
37 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
38 <![CDATA[ |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
39 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
40 **What it does** |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
41 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
42 Tool to select representative sequences from a multiple sequence alignment in clustal format. |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
43 Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries. |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
44 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
45 **Input** |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
46 Multiple sequence alignment in clustal format |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
47 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
48 **Options** |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
49 -n Number of sequences in the output alignment. (Default: 6) |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
50 -i Optimize for this percentage of mean pairwise identity (Default: 80) |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
51 -m Sequences with a higher percentage of pairwise identity will be removed (Default: 95) |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
52 -x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
53 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
54 **Output** |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
55 Clustal alignment with selected sequences |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
56 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
57 ]]> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
58 |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
59 </help> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
60 <citations> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
61 <citation type="doi">10.1093/nar/gkw558</citation> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
62 </citations> |
|
48fc2c21fe1c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
rnateam
parents:
diff
changeset
|
63 </tool> |