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https://github.com/galaxyproject/galaxy.git
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John Chilton
8af243c176
Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions. For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules". This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions. This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running.
141 lines
6.2 KiB
XML
141 lines
6.2 KiB
XML
<?xml version='1.0' encoding='utf-8'?>
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<toolbox monitor="true">
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<section id="getext" name="Get Data">
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<tool file="data_source/upload.xml" />
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<tool file="data_source/ucsc_tablebrowser.xml" />
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<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
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<tool file="data_source/ebi_sra.xml" />
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<tool file="data_source/flymine.xml" />
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<tool file="data_source/fly_modencode.xml" />
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<tool file="data_source/modmine.xml" />
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<tool file="data_source/mousemine.xml" />
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<tool file="data_source/ratmine.xml" />
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<tool file="data_source/yeastmine.xml" />
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<tool file="data_source/worm_modencode.xml" />
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<tool file="data_source/wormbase.xml" />
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<tool file="data_source/zebrafishmine.xml" />
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<tool file="data_source/eupathdb.xml" />
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<tool file="genomespace/genomespace_importer.xml" />
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<tool file="genomespace/genomespace_push.xml" />
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</section>
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<section id="send" name="Send Data">
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<tool file="genomespace/genomespace_exporter.xml" />
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</section>
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<section id="liftOver" name="Lift-Over">
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<tool file="extract/liftOver_wrapper.xml" />
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</section>
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<section id="collection_operations" name="Collection Operations">
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<tool file="${model_tools_path}/unzip_collection.xml" labels="new" />
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<tool file="${model_tools_path}/zip_collection.xml" labels="new" />
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<tool file="${model_tools_path}/filter_failed_collection.xml" labels="new" />
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<tool file="${model_tools_path}/flatten_collection.xml" labels="new" />
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<tool file="${model_tools_path}/merge_collection.xml" labels="new" />
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<tool file="${model_tools_path}/relabel_from_file.xml" />
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<tool file="${model_tools_path}/filter_from_file.xml" />
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<tool file="${model_tools_path}/sort_collection_list.xml" />
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<tool file="${model_tools_path}/apply_rules.xml" />
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</section>
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<section id="textutil" name="Text Manipulation">
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<tool file="filters/fixedValueColumn.xml" />
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<tool file="filters/catWrapper.xml" hidden="true" />
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<tool file="filters/condense_characters.xml" />
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<tool file="filters/convert_characters.xml" />
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<tool file="filters/mergeCols.xml" />
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<tool file="filters/CreateInterval.xml" />
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<tool file="filters/cutWrapper.xml" hidden="true" />
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<tool file="filters/changeCase.xml" />
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<tool file="filters/pasteWrapper.xml" />
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<tool file="filters/remove_beginning.xml" />
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<tool file="filters/randomlines.xml" />
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<tool file="filters/headWrapper.xml" />
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<tool file="filters/tailWrapper.xml" />
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<tool file="filters/trimmer.xml" />
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<tool file="filters/wc_gnu.xml" />
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<tool file="filters/secure_hash_message_digest.xml" />
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</section>
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<section id="convert" name="Convert Formats">
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<tool file="filters/bed2gff.xml" />
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<tool file="filters/gff2bed.xml" />
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<tool file="maf/maf_to_bed.xml" />
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<tool file="maf/maf_to_interval.xml" />
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<tool file="maf/maf_to_fasta.xml" />
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<tool file="filters/sff_extractor.xml" />
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<tool file="filters/wig_to_bigwig.xml" />
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<tool file="filters/bed_to_bigbed.xml" />
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</section>
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<section id="filter" name="Filter and Sort">
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<tool file="stats/filtering.xml" />
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<tool file="filters/sorter.xml" />
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<tool file="filters/grep.xml" />
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<label id="gff" text="GFF" />
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<tool file="filters/gff/extract_GFF_Features.xml" />
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<tool file="filters/gff/gff_filter_by_attribute.xml" />
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<tool file="filters/gff/gff_filter_by_feature_count.xml" />
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<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
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</section>
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<section id="group" name="Join, Subtract and Group">
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<tool file="filters/joiner.xml" />
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<tool file="filters/compare.xml" />
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<tool file="stats/grouping.xml" />
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</section>
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<section id="fetchAlignSeq" name="Fetch Alignments/Sequences">
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<tool file="maf/interval2maf_pairwise.xml" />
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<tool file="maf/interval2maf.xml" />
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<tool file="maf/interval_maf_to_merged_fasta.xml" />
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<tool file="maf/genebed_maf_to_fasta.xml" />
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<tool file="maf/maf_stats.xml" />
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<tool file="maf/maf_thread_for_species.xml" />
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<tool file="maf/maf_limit_to_species.xml" />
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<tool file="maf/maf_limit_size.xml" />
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<tool file="maf/maf_by_block_number.xml" />
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<tool file="maf/maf_filter.xml" />
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<tool file="maf/maf_reverse_complement.xml" />
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<tool file="extract/extract_genomic_dna.xml" />
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</section>
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<section id="bxops" name="Operate on Genomic Intervals" version="">
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<tool file="filters/wiggle_to_simple.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
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<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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</section>
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<section id="stats" name="Statistics">
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<tool file="stats/gsummary.xml" />
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<tool file="filters/uniq.xml" />
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</section>
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<section id="plots" name="Graph/Display Data">
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<tool file="plotting/boxplot.xml" hidden="true" />
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<tool file="maf/vcf_to_maf_customtrack.xml" />
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</section>
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<section id="hgv" name="Phenotype Association">
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<tool file="evolution/codingSnps.xml" />
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<tool file="evolution/add_scores.xml" />
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<tool file="phenotype_association/sift.xml" />
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<tool file="phenotype_association/linkToGProfile.xml" />
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<tool file="phenotype_association/linkToDavid.xml" />
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<tool file="phenotype_association/ldtools.xml" />
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<tool file="phenotype_association/pass.xml" />
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<tool file="phenotype_association/gpass.xml" />
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<tool file="phenotype_association/beam.xml" />
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<tool file="phenotype_association/lps.xml" />
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<tool file="phenotype_association/master2pg.xml" />
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</section>
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<section id="cshl_library_information" name="NGS: QC and manipulation">
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<label id="illumina" text="Illumina data" />
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<label id="454" text="Roche-454 data" />
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<label id="solid" text="AB-SOLiD data" />
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<tool file="next_gen_conversion/solid2fastq.xml" />
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<tool file="solid_tools/solid_qual_stats.xml" />
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<tool file="solid_tools/solid_qual_boxplot.xml" />
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<label id="generic_fastq" text="Generic FASTQ manipulation" />
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<label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" />
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</section>
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<section id="ngs_mapping" name="NGS: Mapping">
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<label id="illumina" text="Illumina" />
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<label id="roche_454" text="Roche-454" />
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<label id="ab_solid" text="AB-SOLiD" />
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</section>
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<label id="deprecated" text="DEPRECATED" />
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<section id="gatk" name="NGS: GATK Tools (beta)">
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</section>
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</toolbox>
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