# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan@bx.psu.edu> # Date 1286458054 14400 # Node ID 3316517f0980642b7706f26ab3a5b4ec461acfde # Parent 9cada14f87657b951ccc9a76af5de03263ba72d9 Enable 'FASTX-Toolkit for FASTQ data' as a subsection under 'NGS: QC and manipulation' in tool_conf.xml.sample/main. --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -218,15 +218,6 @@ <tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <!--<label text="Deprecated: Generic FASTQ data" id="fastq" /> - <tool file="next_gen_conversion/fastq_gen_conv.xml" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="metag_tools/split_paired_reads.xml" - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - --><label text="Roche-454 data" id="454" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /> @@ -244,6 +235,21 @@ <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> + <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> + <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_quality_filter.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> + <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> + <tool file="fastx_toolkit/fastx_clipper.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> + <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><!-- Keep this section commented until it includes tools that --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -305,15 +305,6 @@ <tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <!--<label text="Deprecated: Generic FASTQ data" id="fastq" /> - <tool file="next_gen_conversion/fastq_gen_conv.xml" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="metag_tools/split_paired_reads.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - --><label text="Roche-454 data" id="454" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /> @@ -331,6 +322,21 @@ <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> + <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit_fastq" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> + <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_quality_filter.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> + <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> + <tool file="fastx_toolkit/fastx_clipper.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> + <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><section name="NGS: Mapping" id="ngs_mapping"><label text="Illumina" id="illumina"/>