Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/promoter2.xml @ 19:4cd848c5590b draft
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
| author | peterjc |
|---|---|
| date | Thu, 23 May 2013 12:49:18 -0400 |
| parents | af3174637834 |
| children | a538e182fab3 |
| rev | line source |
|---|---|
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
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1 <tool id="promoter2" name="Promoter 2.0" version="0.0.6"> |
| 7 | 2 <description>Find eukaryotic PolII promoters in DNA sequences</description> |
| 3 <!-- If job splitting is enabled, break up the query file into parts --> | |
| 4 <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal --> | |
| 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> | |
| 6 <command interpreter="python"> | |
| 7 promoter2.py "\$NSLOTS" $fasta_file $tabular_file | |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents:
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8 ##I want the number of threads to be a Galaxy config option... |
| 7 | 9 ##Set the number of threads in the runner entry in universe_wsgi.ini |
| 10 ##which (on SGE at least) will set the $NSLOTS environment variable. | |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents:
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changeset
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11 ##If the environment variable isn't set, get "", and the python wrapper |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents:
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diff
changeset
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12 ##defaults to four threads. |
| 7 | 13 </command> |
| 14 <stdio> | |
| 15 <!-- Anything other than zero is an error --> | |
| 16 <exit_code range="1:" /> | |
| 17 <exit_code range=":-1" /> | |
| 18 </stdio> | |
| 19 <inputs> | |
| 20 <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" /> | |
| 24 </outputs> | |
| 25 <requirements> | |
| 26 <requirement type="binary">promoter</requirement> | |
| 27 </requirements> | |
| 16 | 28 <tests> |
| 29 <test> | |
| 30 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/> | |
| 31 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
| 35 <output name="tabular_file" file="empty_promoter2.tabular" ftype="tabular"/> | |
| 36 </test> | |
| 37 </tests> | |
| 7 | 38 <help> |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model. | |
| 43 | |
| 44 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): | |
| 45 | |
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46 ====== ================================================== |
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4cd848c5590b
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peterjc
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47 Column Description |
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4cd848c5590b
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peterjc
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48 ------ -------------------------------------------------- |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
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49 1 Sequence identifier (first word of FASTA header) |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
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50 2 Promoter position, e.g. 600 |
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4cd848c5590b
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peterjc
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51 3 Promoter score, e.g. 1.063 |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents:
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52 4 Promoter likelihood, e.g. Highly likely prediction |
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4cd848c5590b
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
peterjc
parents:
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53 ====== ================================================== |
| 7 | 54 |
| 55 The scores are classified very simply as follows: | |
| 56 | |
| 57 ========= ======================== | |
| 58 Score Description | |
| 59 --------- ------------------------ | |
| 60 below 0.5 ignored | |
| 61 0.5 - 0.8 Marginal prediction | |
| 62 0.8 - 1.0 Medium likely prediction | |
| 63 above 1.0 Highly likely prediction | |
| 64 ========= ======================== | |
| 65 | |
| 66 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. | |
| 67 | |
| 68 **References** | |
| 69 | |
| 70 Knudsen. | |
| 71 Promoter2.0: for the recognition of PolII promoter sequences. | |
| 72 Bioinformatics, 15:356-61, 1999. | |
| 73 http://dx.doi.org/10.1093/bioinformatics/15.5.356 | |
| 74 | |
| 75 http://www.cbs.dtu.dk/services/Promoter/output.php | |
| 76 | |
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af3174637834
Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
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77 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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af3174637834
Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
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78 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
| 7 | 79 </help> |
| 80 </tool> |