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Enable 'FASTX-Toolkit for FASTQ data' as a subsection under 'NGS: QC and manipulation' in tool_conf.xml.sample/main.

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This commit is contained in:
Daniel Blankenberg
2010-10-07 09:27:34 -04:00
parent 9c7065d898
commit 3293abc9b4
2 changed files with 30 additions and 18 deletions
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tool_conf.xml.main
+15 -9
View File
@@ -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"/>
tool_conf.xml.sample
+15 -9
View File
@@ -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