Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/promoter2.xml @ 34:7a2e20baacee draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"v0.2.13 - Python 3 fix for raising StopIteration"
author peterjc
date Thu, 17 Jun 2021 17:58:23 +0000
parents 20da7f48b56f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
34
7a2e20baacee "v0.2.13 - Python 3 fix for raising StopIteration"
peterjc
parents: 32
diff changeset
1 <tool id="promoter2" name="Promoter 2.0" version="0.0.13">
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
2 <description>Find eukaryotic PolII promoters in DNA sequences</description>
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
3 <!-- If job splitting is enabled, break up the query file into parts -->
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
4 <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
26
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
6 <requirements>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
7 <requirement type="package">promoter</requirement>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
8 </requirements>
30
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
9 <version_command>
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
10 python $__tool_directory__/promoter2.py --version
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
11 </version_command>
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
12 <command detect_errors="aggressive">
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
13 python $__tool_directory__/promoter2.py "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
14 </command>
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
15 <inputs>
30
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
16 <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/>
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
17 </inputs>
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
18 <outputs>
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
19 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
20 </outputs>
16
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
21 <tests>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
22 <test>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
23 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
24 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
25 </test>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
26 <test>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
27 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
28 <output name="tabular_file" file="empty_promoter2.tabular" ftype="tabular"/>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
29 </test>
1d5486a02bc4 Uploaded v0.2.4, added unit tests for Promoter 2
peterjc
parents: 7
diff changeset
30 </tests>
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
31 <help>
30
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
32
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
33 **What it does**
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
34
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
35 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
36
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
37 The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
38
19
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
39 ====== ==================================================
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
40 Column Description
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
41 ------ --------------------------------------------------
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
42 1 Sequence identifier (first word of FASTA header)
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
43 2 Promoter position, e.g. 600
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
44 3 Promoter score, e.g. 1.063
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
45 4 Promoter likelihood, e.g. Highly likely prediction
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents: 17
diff changeset
46 ====== ==================================================
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
47
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
48 The scores are classified very simply as follows:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
49
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
50 ========= ========================
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
51 Score Description
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
52 --------- ------------------------
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
53 below 0.5 ignored
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
54 0.5 - 0.8 Marginal prediction
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
55 0.8 - 1.0 Medium likely prediction
30
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 28
diff changeset
56 above 1.0 Highly likely prediction
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
57 ========= ========================
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
58
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
59 Internally the input FASTA file is divided into parts (to allow multiple processors to be used), and the raw output is reformatted into this tabular layout suitable for downstream analysis within Galaxy.
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
60
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
61 **References**
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
62
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
63 If you use this Galaxy tool in work leading to a scientific publication please
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
64 cite the following papers:
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
65
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
66 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
67 Galaxy tools and workflows for sequence analysis with applications
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
68 in molecular plant pathology. PeerJ 1:e167
32
20da7f48b56f "Check this is up to date with all 2020 changes"
peterjc
parents: 30
diff changeset
69 https://doi.org/10.7717/peerj.167
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
70
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
71 Steen Knudsen (1999).
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
72 Promoter2.0: for the recognition of PolII promoter sequences.
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
73 Bioinformatics, 15:356-61.
32
20da7f48b56f "Check this is up to date with all 2020 changes"
peterjc
parents: 30
diff changeset
74 https://doi.org/10.1093/bioinformatics/15.5.356
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
75
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 19
diff changeset
76 See also http://www.cbs.dtu.dk/services/Promoter/output.php
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
77
17
af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
parents: 16
diff changeset
78 This wrapper is available to install into other Galaxy Instances via the Galaxy
af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
parents: 16
diff changeset
79 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
80 </help>
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
81 <citations>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
82 <citation type="doi">10.7717/peerj.167</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
83 <citation type="doi">10.1093/bioinformatics/15.5.356</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
84 </citations>
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents:
diff changeset
85 </tool>