details: http://www.bx.psu.edu/hg/galaxy/rev/1fa410dd1aa1 changeset: 2845:1fa410dd1aa1 user: Anton Nekrutenko anton@bx.psu.edu date: Thu Oct 08 09:01:19 2009 -0400 description: added space to paste tool, removed old solexa tool, fixes fastq stat test

4 file(s) affected in this change:

tool_conf.xml.sample tools/fastx_toolkit/fastx_quality_statistics.xml tools/filters/pasteWrapper.pl tools/filters/pasteWrapper.xml

diffs (69 lines):

diff -r e73efc9387ee -r 1fa410dd1aa1 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Oct 07 16:37:48 2009 -0400 +++ b/tool_conf.xml.sample Thu Oct 08 09:01:19 2009 -0400 @@ -64,7 +64,6 @@ <tool file="filters/axt_to_lav.xml" /> <tool file="filters/bed2gff.xml" /> <tool file="fasta_tools/fasta_to_tabular.xml" /> - <tool file="metag_tools/fastqsolexa_to_fasta_qual.xml" /> <tool file="filters/gff2bed.xml" /> <tool file="filters/lav_to_bed.xml" /> <tool file="maf/maf_to_bed.xml" /> diff -r e73efc9387ee -r 1fa410dd1aa1 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Wed Oct 07 16:37:48 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Thu Oct 08 09:01:19 2009 -0400 @@ -9,7 +9,7 @@

<tests> <test> - <param name="input" value="fastq_stats1.fastq" /> + <param name="input" value="fastq_stats1.fastq" ftype="fastq"/> <param name="offset" value="64" /> <output name="output" file="fastq_stats1.out" /> </test> diff -r e73efc9387ee -r 1fa410dd1aa1 tools/filters/pasteWrapper.pl --- a/tools/filters/pasteWrapper.pl Wed Oct 07 16:37:48 2009 -0400 +++ b/tools/filters/pasteWrapper.pl Thu Oct 08 09:01:19 2009 -0400 @@ -4,7 +4,7 @@ use warnings; my $command = ""; # a wrapper for paste for use in galaxy -# lessWrapper.pl [filename1] [filename2] [delimiter] [output] +# pasteWrapper.pl [filename1] [filename2] [delimiter] [output]

die "Check arguments" unless @ARGV == 4;

@@ -20,18 +20,12 @@ $command = "paste -d "|" $ARGV[0] $ARGV[1]"; } elsif ($ARGV[2] eq 'Dt') { $command = "paste -d "." $ARGV[0] $ARGV[1]"; +} elsif ($ARGV[2] eq 'Sp') { + $command = "paste -d " " $ARGV[0] $ARGV[1]"; } - -

open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; open (PASTE, "$command |") or die "Cannot run paste:$!\n"; - - - - - -

while (<PASTE>) { print OUT; diff -r e73efc9387ee -r 1fa410dd1aa1 tools/filters/pasteWrapper.xml --- a/tools/filters/pasteWrapper.xml Wed Oct 07 16:37:48 2009 -0400 +++ b/tools/filters/pasteWrapper.xml Thu Oct 08 09:01:19 2009 -0400 @@ -11,7 +11,8 @@ <option value="C">Comma</option> <option value="D">Dash</option> <option value="U">Underscore</option> - <option value="P">Pipe</option> + <option value="P">Pipe</option> + <option value="Sp">Space</option> </param> </inputs> <outputs>