Mercurial > repos > iracooke > make_protein_decoys
changeset 0:a90539d8e409 draft
Uploaded
| author | iracooke |
|---|---|
| date | Fri, 13 Jun 2014 18:10:03 -0400 |
| parents | |
| children | 354e820eb485 |
| files | README README.md make_decoy.xml repository_dependencies.xml |
| diffstat | 4 files changed, 49 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Jun 13 18:10:03 2014 -0400 @@ -0,0 +1,4 @@ +Requirements: +This package uses protk which must be installed separately. + +For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jun 13 18:10:03 2014 -0400 @@ -0,0 +1,3 @@ +# Make decoys from a protein database + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_decoy.xml Fri Jun 13 18:10:03 2014 -0400 @@ -0,0 +1,38 @@ +<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0"> + <requirements> + <requirement type="package" version="1.3">protk</requirement> + </requirements> + + <description> + Generate random protein sequences with the same AA composition as input sequences + </description> + + <command> + make_decoy.rb $fasta_file -o $output -P $prefix_string $append + </command> + + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> + <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> + <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> + </inputs> + + <outputs> + <data format="fasta" name="output" /> + </outputs> + + + <help> + +**What it does** + +Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches + + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Jun 13 18:10:03 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </repositories>