| Previous changeset 0:83173eca36b7 (2012-07-24) Next changeset 2:a104cc98359c (2012-07-24) |
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Commit message:
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added:
synapse_download.xml |
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| diff -r 83173eca36b7 -r 7a60e992bfb0 synapse_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_download.xml Tue Jul 24 17:34:14 2012 -0400 |
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| @@ -0,0 +1,74 @@ +<tool id="synapse_download" name="Synapse Download" version="1.0"> + <description>Download Synapse Entity</description> + <command interpreter="python">$script_file +#if str( $user ) != '': + -u "$user" +#end if +#if str( $pass ) != '': + -p "$pass" +#end if +-s $synid +$data_type +-o $outfile + </command> + <inputs> + <param name="user" type="text" size="90" label="Username"/> + <param name="pass" type="text" size="90" label="Password"/> + <param name="synid" type="text" label="Synapse ID"/> + <param name="data_type" type="select" label="Data Type"> + <option value="-e">Affy Eset</option> + <option value="-a">Attachment</option> + </param> + </inputs> + <outputs> + <data format="txt" name="outfile" label="${synid}" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode = """ +library('getopt'); +library(affy) +require(synapseClient) + +opt = getopt(c( + 'user', 'u', 2, "character", + 'pass', 'p', 2, "character", + 'outfile', 'o', 2, "character", + 'synid', 's', 2, "character", + 'eset', 'e', 0, "logical", + 'attach', 'a', 0, "logical" +)); + +if ( !is.null(opt\$user) && !is.null(opt\$pass)) { + synapseLogin(username=user, password=pass) +} + +ent <- loadEntity(opt\$synid); + +if (!is.null(opt\$eset)) { + eset <- exprs(ent\$objects\$eset); + write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file=opt\$outfile) + write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE); +} +if (!is.null(opt\$attach)) { + fpath <- file.path(ent\$cacheDir, ent\$files[[1]]); + file.copy(fpath, opt\$outfile, overwrite=T); +} + +""" + +import tempfile +import os +import sys +import subprocess + +h, path = tempfile.mkstemp() +os.write(h,rcode) +os.close(h) + +print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT ) +os.unlink(path) + +]]></configfile> + </configfiles> +</tool> |