Mercurial > repos > joachim-jacob > blat
changeset 1:da4426cac227 draft
Fixed tests
author | Joachim Jacob <joachim.jacob@gmail.com> |
---|---|
date | Wed, 24 Jul 2013 16:23:44 +0200 |
parents | 3cec538aab33 |
children | df0c23b49a81 |
files | blat_wrapper.pl blat_wrapper.xml |
diffstat | 2 files changed, 37 insertions(+), 36 deletions(-) [+] |
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--- a/blat_wrapper.pl Thu May 30 07:13:55 2013 -0400 +++ b/blat_wrapper.pl Wed Jul 24 16:23:44 2013 +0200 @@ -28,16 +28,14 @@ ######################################################################## my ($configfile) = @ARGV; my (%para); -open(CONFIG,"<$configfile"); +open(CONFIG,"<",$configfile); while (<CONFIG>) { if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; } } close(CONFIG); =Excerpt Config parameters - ## first we pass some galaxy environment variables - galtemp==${__new_file_path__} - + ## first we pass some galaxy environment variables galtemp==${__new_file_path__} @@ -76,7 +74,6 @@ INFO "$para\tset to\t$para{$para}"; } - # ---------------------- Prepping temp dir ----------------------------# ######################################################################## # within the temporary directory of Galaxy, we create a temporary dir @@ -90,10 +87,14 @@ mkdir "$tempdir", 077 unless -d "$tempdir"; INFO "\nTemporary directory:\n$tempdir"; +# --------------------- Checking executable ---------------------------# +######################################################################## +#~ my $command = "which blat "; +#~ run_process($command, "Testing path", $tempdir); # -------------------- Assembling command ----------------------------# ######################################################################## -my $command = "blat "; # this will ultimately be executed +my $command = "blat "; # this will ultimately be executed $command .= " $para{'referencepath'}"; if ( $para{'range'} ) { ## format checking of the provided range @@ -118,7 +119,7 @@ if ( $para{'advanced_params.use'} eq "yes" ){ delete($para{'advanced_params.use'}); - $command .= " -minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'} -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} -stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} "; + $command .= " -minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'} -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} -stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} "; if($para{'repeats'} eq 'yes' ){ $command .= " -repeats=$para{'qMask'}"; }
--- a/blat_wrapper.xml Thu May 30 07:13:55 2013 -0400 +++ b/blat_wrapper.xml Wed Jul 24 16:23:44 2013 +0200 @@ -1,20 +1,19 @@ -<tool id="blat" name="Align sequences with BLAT" version="1.0.0"> + +<tool id="blat" name="Align sequences with BLAT" version="1.0.1"> <!-- Additional info: wrapper compatible with versions ..... --> <description> to a reference genome </description> - <version_command/> + <version_command> + </version_command> <requirements> <requirement type="package" version="1.0.0">blat</requirement> </requirements> <command interpreter="perl"> - ## it is recommended that you write a wrapper for your tool - ## and pass all parameters to that tool, which parses them. blat_wrapper.pl $configfile - </command> <inputs> @@ -42,7 +41,7 @@ </param> </when> <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the sequence database" /> + <param name="ownFile" type="data" format="fasta" metadata_nameloc="dbkey" label="Select the sequence database" /> </when> <!-- history --> </conditional> <!-- refGenomeSource --> @@ -136,30 +135,31 @@ </configfile> </configfiles> - <tests> + <tests> <test> - <param name="input" value="input83.fas" /> - <param name="refGenomeSource.genomeSource" value="history" /> - <param name="refGenomeSource.ownFile" value="databasetest1.txt" /> - <param name="q" value="dna" /> - <param name="t" value="dna" /> - <param name="advanced_params.use" value="yes" /> - <param name="advanced_params.tileSize" value="11" /> - <param name="advanced_params.stepSize" value="11" /> - <param name="advanced_params.oneOff" value="0" /> - <param name="advanced_params.minMatch" value="2" /> - <param name="advanced_params.minScore" value="30" /> - <param name="advanced_params.maxGap" value="2" /> - <param name="advanced_params.mask" value="lower" /> - <param name="advanced_params.qMask" value="lower" /> - <param name="advanced_params.repeats" value="no" /> - <param name="advanced_params.trimT" value="no" /> - <param name="advanced_params.noTrimA" value="yes" /> - <param name="advanced_params.fine" value="no" /> - <param name="advanced_params.maxIntron" value="750000" /> - <param name="advanced_params.extendThroughN" value="no" /> - <output name="output" file="outputtest1.txt" lines_diff="2"/> - </test> + <param name="input" value="input83.fas" ftype="fasta" /> + <param name="q" value="dna" /> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="blatdatabase1.fas" /> + <param name="t" value="dna" /> + <param name="use" value="yes" /> + <param name="tileSize" value="11" /> + <param name="stepSize" value="11" /> + <param name="oneOff" value="0" /> + <param name="tileSize" value="11" /> + <param name="minMatch" value="2" /> + <param name="minScore" value="30" /> + <param name="maxGap" value="2" /> + <param name="mask" value="lower" /> + <param name="qMask" value="lower" /> + <param name="repeats" value="no" /> + <param name="trimT" value="yes" /> + <param name="noTrimA" value="no" /> + <param name="fine" value="no" /> + <param name="maxIntron" value="750000" /> + <param name="extendThroughN" value="no" /> + <output name="output" file="blatoutput1.txt" ftype="tabular" lines_diff="2"/> + </test> </tests> <help>