details: http://www.bx.psu.edu/hg/galaxy/rev/2fb0a64c6aaa changeset: 2835:2fb0a64c6aaa user: guru date: Tue Oct 06 16:55:47 2009 -0400 description: Fixing broken tool configs 3 file(s) affected in this change: tools/fastx_toolkit/fastx_reverse_complement.xml tools/fastx_toolkit/fastx_trimmer.xml tools/filters/trimmer.xml diffs (35 lines): diff -r b14f99a4f736 -r 2fb0a64c6aaa tools/fastx_toolkit/fastx_reverse_complement.xml --- a/tools/fastx_toolkit/fastx_reverse_complement.xml Tue Oct 06 15:00:32 2009 -0400 +++ b/tools/fastx_toolkit/fastx_reverse_complement.xml Tue Oct 06 16:55:47 2009 -0400 @@ -47,6 +47,7 @@ TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA +CSHL_1_FC42AGWWWXX:8:1:3:740 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 + ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. diff -r b14f99a4f736 -r 2fb0a64c6aaa tools/fastx_toolkit/fastx_trimmer.xml --- a/tools/fastx_toolkit/fastx_trimmer.xml Tue Oct 06 15:00:32 2009 -0400 +++ b/tools/fastx_toolkit/fastx_trimmer.xml Tue Oct 06 16:55:47 2009 -0400 @@ -3,7 +3,7 @@ <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command> <inputs> - <param format="fasta,fastasanger" name="input" type="data" label="Library to clip" /> + <param format="fasta,fastqsanger" name="input" type="data" label="Library to clip" /> <param name="first" size="4" type="integer" value="1"> <label>First base to keep</label> diff -r b14f99a4f736 -r 2fb0a64c6aaa tools/filters/trimmer.xml --- a/tools/filters/trimmer.xml Tue Oct 06 15:00:32 2009 -0400 +++ b/tools/filters/trimmer.xml Tue Oct 06 16:55:47 2009 -0400 @@ -4,7 +4,7 @@ trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 </command> <inputs> - <param format="tabular,text" name="input1" type="data" label="this dataset"/> + <param format="tabular,txt" name="input1" type="data" label="this dataset"/> <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/>