Mercurial > repos > swebb > pycrac
diff pyCRAC/pyAlignment2Tab.xml @ 0:19b20927172d draft
Uploaded
| author | swebb |
|---|---|
| date | Tue, 18 Jun 2013 09:11:00 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyCRAC/pyAlignment2Tab.xml Tue Jun 18 09:11:00 2013 -0400 @@ -0,0 +1,139 @@ +<tool id="pyAlignment2Tab" name="pyAlignment2Tab"> + <description>converter</description> + <requirements> + <requirement type="package">pyCRAC</requirement> + </requirements> + <command interpreter="python">/usr/local/bin/pyAlignment2Tab.py -f $input --limit $limit -o $output --singlefile + </command> + <version_command>/usr/local/bin/pyAlignment2Tab.py --version</version_command> + <inputs> + <param name="input" type="data" format="fasta" label="pyReadAligner output file -f" help="Fasta file"/> + <param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50"> + <validator type="in_range" min="50" message="Please enter a value greater than 50"/> + </param> + <param name="label" type="text" format="txt" size="30" value="pyAlignment2Tab" label="Enter output file label -o" /> + </inputs> + <outputs> + <data name="output" format="txt" label="${label.value}.tab"/> + </outputs> + <help> + +.. class:: infomark + +**pyAlignment2Tab** + +pyAlignment2Tab is part of the pyCRAC_ package. Converts pyReadAligner fasta output to a tabular alignment output. + +Example:: + + The tool expects a standard pyReadAligner fasta-formatted output file: + + >GeneX + ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAACAGCAGCAGCGAGAGTAGTAGTAACAAAAACAATATCAATGTCGGCGTCGGTGACGATAGCGGTAA + >257930-10 + ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT---------------------------------------------------------------------------------------------------------------- + >3664964-1 + ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT---------------------------------------------------------------------------------------------------------------- + >4033560-1 + ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT---------------------------------------------------------------------------------------------------------------- + >8571880-1 + ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT---------------------------------------------------------------------------------------------------------------- + >9617396-1 + ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT---------------------------------------------------------------------------------------------------------------- + >843368-5 + ------------AACAcGGATACAAGACACGCACATTCTG------------------------------------------------------------------------------------------------------------------- + >854553-5 + ------------AACATGGATACAAGACACGCAC--TCTG------------------------------------------------------------------------------------------------------------------- + >1522401-2 + --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA----------------------------------------------------------------------------------------------------- + >5981234-1 + --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- + >997684-4 + --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- + >1046653-4 + ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC---------------------------------------------------------------------------------------------------- + >1103730-4 + ---------------ATGGATACAAGACACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- + >1603913-2 + ---------------ATGGATACAAGAaACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- + >180349-12 + ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG----------------------------------------------------------------------------------------------------------- + >1985106-1 + ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC---------------------------------------------------------------------------------------------------- + >1987775-1 + ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC---------------------------------------------------------------------------------------------------- + >2258725-1 + ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC---------------------------------------------------------------------------------------------------- + >2631987-1 + ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC---------------------------------------------------------------------------------------------------- + + This will be converted into: + + 1 .........|.........|.........|.........|.........|.........|.........|.........|.........| 90 + >GeneX ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAAC + >257930-10 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT----------------------------------------------- + >3664964-1 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT----------------------------------------------- + >4033560-1 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT----------------------------------------------- + >8571880-1 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT----------------------------------------------- + >9617396-1 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT----------------------------------------------- + >843368-5 ------------AACAcGGATACAAGACACGCACATTCTG-------------------------------------------------- + >854553-5 ------------AACATGGATACAAGACACGCAC--TCTG-------------------------------------------------- + >1522401-2 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA------------------------------------ + >5981234-1 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA------------------------------------ + >997684-4 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA------------------------------------ + >1046653-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC----------------------------------- + >1103730-4 ---------------ATGGATACAAGACACGCACAcTCTG-------------------------------------------------- + >1603913-2 ---------------ATGGATACAAGAaACGCACAcTCTG-------------------------------------------------- + >180349-12 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG------------------------------------------ + >1985106-1 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC----------------------------------- + >1987775-1 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC----------------------------------- + >2258725-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC----------------------------------- + >2631987-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC----------------------------------- + >337206-9 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCAC----------------------------------- + >4616761-1 ---------------ATGGATAgAAGACACGCACATTCTGCTTTACTGGtAGCAC----------------------------------- + >4756312-1 ---------------ATGGATACAAcACACGCACAcTCTG-------------------------------------------------- + >4763682-1 ---------------ATGGATACAAGACACGCACATTCcGCTTTcCTG------------------------------------------ + >5971268-1 ---------------ATGGATACAAGACACGCACATTCcGCTcTACTc------------------------------------------ + >6644790-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTcGCAGCAC----------------------------------- + >7112423-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGtCAGCAC----------------------------------- + >7559990-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCcGgAC----------------------------------- + >8007281-1 ---------------ATGGATAtAAGACACGCACAcTCTG-------------------------------------------------- + >9150255-1 ---------------ATGGATACAcGACACGCACATTCcGCTTTcCTG------------------------------------------ + >9180814-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgcC----------------------------------- + >963117-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGCAC----------------------------------- + >9672073-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCcC----------------------------------- + >971218-4 ---------------ATGGATACAAGACACGCACATcCTGCTTTACTGG-AGCACC---------------------------------- + >10040274-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGgACCACA------------------------------- + >1063072-4 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCACCACA------------------------------- + >1430188-2 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACA------------------------------- + >5196741-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCcGCACCACA------------------------------- + >6017337-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGtCAGaACCcCA------------------------------- + >7159053-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCcaA------------------------------- + >7528336-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCAaCACA------------------------------- + >735584-6 --------------------------------------------------------ACAGAGTGCTACTGCAAAcAGCAGGAGCAGCAAC + >8551047-1 --------------------------------------------------------ACAGAGTGCTAtTGCAAAcAGCAGGAGtAGtAAC + >3000121-1 ------------------------------------------------------------AGTcCTACcGCAAATAGCAGcAGCAGCAAC + >928481-5 ------------------------------------------------------------AGTGCTACcGCAAATAGCAGGAGCAGCAAC + >126987-15 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC + >3122797-1 ----------------------------------------------------------------------CAAATAGCAGGcGCAGCAAC + >6684686-1 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC + + Note that the column width here was set to 90 characters + +.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html + +------ + +**Parameter list** + +Options:: + + -f data.fasta + Type the path to the fasta file that you want to use. + --limit=90 + Allows the user to set the column width of the alignment. Default=90 characters + -o output.fasta + Provide the name of your output file + + </help> +</tool>