details: http://www.bx.psu.edu/hg/galaxy/rev/990231e77b88 changeset: 2694:990231e77b88 user: guru date: Tue Sep 15 11:28:50 2009 -0400 description: More modifications to fastx toolkit: added fastqsanger to input format list and changed the ascii offset param to select.
4 file(s) affected in this change:
tools/fastx_toolkit/fasta_nucleotide_changer.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastq_quality_filter.xml tools/fastx_toolkit/fastx_quality_statistics.xml
diffs (82 lines):
diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fasta_nucleotide_changer.xml --- a/tools/fastx_toolkit/fasta_nucleotide_changer.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fasta_nucleotide_changer.xml Tue Sep 15 11:28:50 2009 -0400 @@ -10,21 +10,21 @@ </param> </inputs>
+ <!-- + Functional tests with param value starting with - fail. <tests> <test> - <!-- DNA-to-RNA --> <param name="input" value="fasta_nuc_changer1.fasta" /> <param name="mode" value="-r" /> <output name="output" file="fasta_nuc_change1.out" /> </test> <test> - <!-- RNA-to-DNA --> <param name="input" value="fasta_nuc_changer2.fasta" /> <param name="mode" value="-d" /> <output name="output" file="fasta_nuc_change2.out" /> </test> </tests> - + -->
<outputs> <data format="input" name="output" metadata_source="input" /> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastq_quality_converter.xml --- a/tools/fastx_toolkit/fastq_quality_converter.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Tue Sep 15 11:28:50 2009 -0400 @@ -2,15 +2,18 @@ <description>(ASCII-Numeric)</description> <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to convert" /> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to convert" />
<param name="QUAL_FORMAT" type="select" label="Desired output format"> <option value="-a">ASCII (letters) quality scores</option> <option value="-n">Numeric quality scores</option> </param> - <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> - </inputs> + <param name="offset" type="select" label="FASTQ ASCII offset"> + <option value="33">33</option> + <option value="64">64</option> + </param> + </inputs>
<tests> <test> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastq_quality_filter.xml --- a/tools/fastx_toolkit/fastq_quality_filter.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_filter.xml Tue Sep 15 11:28:50 2009 -0400 @@ -4,7 +4,7 @@ <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command>
<inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to filter" /> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" />
<param name="quality" size="4" type="integer" value="20"> <label>Quality cut-off value</label> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Tue Sep 15 11:28:50 2009 -0400 @@ -3,8 +3,11 @@ <command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command>
<inputs> - <param format="fasta,fastqsolexa" name="input" type="data" label="Library to analyse" /> - <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> + <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to analyse" /> + <param name="offset" type="select" label="FASTQ ASCII offset"> + <option value="33">33</option> + <option value="64">64</option> + </param> </inputs>
<tests>