Mercurial > repos > mingchen0919 > mygene_and_myvariant
changeset 1:f8ac93c41720 draft
special characters
| author | mingchen0919 |
|---|---|
| date | Tue, 20 Mar 2018 13:59:04 -0400 |
| parents | a88f12177e6f |
| children | a00a424ff951 |
| files | helper.R mygene_and_myvariant_macros.xml variant_simple_search.Rmd variant_simple_search.csv variant_simple_search.xml variant_simple_search_render.R |
| diffstat | 6 files changed, 1525 insertions(+), 27 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/helper.R Tue Mar 20 13:59:04 2018 -0400 @@ -0,0 +1,28 @@ +#' \code{getopt_specification_matrix} returns a getopt specification matrix. +#' +#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. +#' The first column are short flags, the second column are argument masks, the third column +#' is data types. The fourth column are variable names used in the tool XML. These three columns are required. +#' @param gtg_name the name of a running GTG. +getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) { + df = read.csv(paste0(tool_dir, specification_file), + header = TRUE, stringsAsFactors = FALSE) + # check if there are duplicated short flags + short_flags = df[, 1] + if (length(unique(short_flags)) < length(short_flags)) { + cat('----Duplicated short flags found ----\n') + cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') + stop('Duplicated short flags are not allowed.') + } + + # use short flags to generate long flags + long_flags = paste0('X_', df[, 1]) + + # specification matrix + df2 = data.frame(long_flags = long_flags, + short_flags = df[, 1], + argument_mask = df[, 2], + data_type = df[, 3]) + + as.matrix(df2) +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mygene_and_myvariant_macros.xml Tue Mar 20 13:59:04 2018 -0400 @@ -0,0 +1,1439 @@ +<macros> + <xml name="fields"> + <option value="cadd" selected="false">cadd</option> + <option value="cadd.1000g" selected="false">cadd.1000g</option> + <option value="cadd.1000g.af" selected="false">cadd.1000g.af</option> + <option value="cadd.1000g.afr" selected="false">cadd.1000g.afr</option> + <option value="cadd.1000g.amr" selected="false">cadd.1000g.amr</option> + <option value="cadd.1000g.asn" selected="false">cadd.1000g.asn</option> + <option value="cadd.1000g.eur" selected="false">cadd.1000g.eur</option> + <option value="cadd.alt" selected="false">cadd.alt</option> + <option value="cadd.anc" selected="false">cadd.anc</option> + <option value="cadd.annotype" selected="false">cadd.annotype</option> + <option value="cadd.bstatistic" selected="false">cadd.bstatistic</option> + <option value="cadd.chmm" selected="false">cadd.chmm</option> + <option value="cadd.chmm.bivflnk" selected="false">cadd.chmm.bivflnk</option> + <option value="cadd.chmm.enh" selected="false">cadd.chmm.enh</option> + <option value="cadd.chmm.enhbiv" selected="false">cadd.chmm.enhbiv</option> + <option value="cadd.chmm.het" selected="false">cadd.chmm.het</option> + <option value="cadd.chmm.quies" selected="false">cadd.chmm.quies</option> + <option value="cadd.chmm.reprpc" selected="false">cadd.chmm.reprpc</option> + <option value="cadd.chmm.reprpcwk" selected="false">cadd.chmm.reprpcwk</option> + <option value="cadd.chmm.tssa" selected="false">cadd.chmm.tssa</option> + <option value="cadd.chmm.tssaflnk" selected="false">cadd.chmm.tssaflnk</option> + <option value="cadd.chmm.tssbiv" selected="false">cadd.chmm.tssbiv</option> + <option value="cadd.chmm.tx" selected="false">cadd.chmm.tx</option> + <option value="cadd.chmm.txflnk" selected="false">cadd.chmm.txflnk</option> + <option value="cadd.chmm.txwk" selected="false">cadd.chmm.txwk</option> + <option value="cadd.chmm.znfrpts" selected="false">cadd.chmm.znfrpts</option> + <option value="cadd.chrom" selected="false">cadd.chrom</option> + <option value="cadd.consdetail" selected="false">cadd.consdetail</option> + <option value="cadd.consequence" selected="false">cadd.consequence</option> + <option value="cadd.consscore" selected="false">cadd.consscore</option> + <option value="cadd.cpg" selected="false">cadd.cpg</option> + <option value="cadd.dna" selected="false">cadd.dna</option> + <option value="cadd.dna.helt" selected="false">cadd.dna.helt</option> + <option value="cadd.dna.mgw" selected="false">cadd.dna.mgw</option> + <option value="cadd.dna.prot" selected="false">cadd.dna.prot</option> + <option value="cadd.dna.roll" selected="false">cadd.dna.roll</option> + <option value="cadd.dst2splice" selected="false">cadd.dst2splice</option> + <option value="cadd.dst2spltype" selected="false">cadd.dst2spltype</option> + <option value="cadd.encode" selected="false">cadd.encode</option> + <option value="cadd.encode.exp" selected="false">cadd.encode.exp</option> + <option value="cadd.encode.h3k27ac" selected="false">cadd.encode.h3k27ac</option> + <option value="cadd.encode.h3k4me1" selected="false">cadd.encode.h3k4me1</option> + <option value="cadd.encode.h3k4me3" selected="false">cadd.encode.h3k4me3</option> + <option value="cadd.encode.nucleo" selected="false">cadd.encode.nucleo</option> + <option value="cadd.encode.occ" selected="false">cadd.encode.occ</option> + <option value="cadd.encode.p_val" selected="false">cadd.encode.p_val</option> + <option value="cadd.encode.p_val.comb" selected="false">cadd.encode.p_val.comb</option> + <option value="cadd.encode.p_val.ctcf" selected="false">cadd.encode.p_val.ctcf</option> + <option value="cadd.encode.p_val.dnas" selected="false">cadd.encode.p_val.dnas</option> + <option value="cadd.encode.p_val.faire" selected="false">cadd.encode.p_val.faire</option> + <option value="cadd.encode.p_val.mycp" selected="false">cadd.encode.p_val.mycp</option> + <option value="cadd.encode.p_val.polii" selected="false">cadd.encode.p_val.polii</option> + <option value="cadd.encode.sig" selected="false">cadd.encode.sig</option> + <option value="cadd.encode.sig.ctcf" selected="false">cadd.encode.sig.ctcf</option> + <option value="cadd.encode.sig.dnase" selected="false">cadd.encode.sig.dnase</option> + <option value="cadd.encode.sig.faire" selected="false">cadd.encode.sig.faire</option> + <option value="cadd.encode.sig.myc" selected="false">cadd.encode.sig.myc</option> + <option value="cadd.encode.sig.polii" selected="false">cadd.encode.sig.polii</option> + <option value="cadd.esp" selected="false">cadd.esp</option> + <option value="cadd.esp.af" selected="false">cadd.esp.af</option> + <option value="cadd.esp.afr" selected="false">cadd.esp.afr</option> + <option value="cadd.esp.eur" selected="false">cadd.esp.eur</option> + <option value="cadd.exon" selected="false">cadd.exon</option> + <option value="cadd.fitcons" selected="false">cadd.fitcons</option> + <option value="cadd.gc" selected="false">cadd.gc</option> + <option value="cadd.gene" selected="false">cadd.gene</option> + <option value="cadd.gene.ccds_id" selected="false">cadd.gene.ccds_id</option> + <option value="cadd.gene.cds" selected="false">cadd.gene.cds</option> + <option value="cadd.gene.cds.cdna_pos" selected="false">cadd.gene.cds.cdna_pos</option> + <option value="cadd.gene.cds.cds_pos" selected="false">cadd.gene.cds.cds_pos</option> + <option value="cadd.gene.cds.rel_cdna_pos" selected="false">cadd.gene.cds.rel_cdna_pos</option> + <option value="cadd.gene.cds.rel_cds_pos" selected="false">cadd.gene.cds.rel_cds_pos</option> + <option value="cadd.gene.feature_id" selected="false">cadd.gene.feature_id</option> + <option value="cadd.gene.gene_id" selected="false">cadd.gene.gene_id</option> + <option value="cadd.gene.genename" selected="false">cadd.gene.genename</option> + <option value="cadd.gene.prot" selected="false">cadd.gene.prot</option> + <option value="cadd.gene.prot.domain" selected="false">cadd.gene.prot.domain</option> + <option value="cadd.gene.prot.protpos" selected="false">cadd.gene.prot.protpos</option> + <option value="cadd.gene.prot.rel_prot_pos" selected="false">cadd.gene.prot.rel_prot_pos</option> + <option value="cadd.gerp" selected="false">cadd.gerp</option> + <option value="cadd.gerp.n" selected="false">cadd.gerp.n</option> + <option value="cadd.gerp.rs" selected="false">cadd.gerp.rs</option> + <option value="cadd.gerp.rs_pval" selected="false">cadd.gerp.rs_pval</option> + <option value="cadd.gerp.s" selected="false">cadd.gerp.s</option> + <option value="cadd.grantham" selected="false">cadd.grantham</option> + <option value="cadd.intron" selected="false">cadd.intron</option> + <option value="cadd.isderived" selected="false">cadd.isderived</option> + <option value="cadd.isknownvariant" selected="false">cadd.isknownvariant</option> + <option value="cadd.istv" selected="false">cadd.istv</option> + <option value="cadd.length" selected="false">cadd.length</option> + <option value="cadd.mapability" selected="false">cadd.mapability</option> + <option value="cadd.mapability.20bp" selected="false">cadd.mapability.20bp</option> + <option value="cadd.mapability.35bp" selected="false">cadd.mapability.35bp</option> + <option value="cadd.min_dist_tse" selected="false">cadd.min_dist_tse</option> + <option value="cadd.min_dist_tss" selected="false">cadd.min_dist_tss</option> + <option value="cadd.mirsvr" selected="false">cadd.mirsvr</option> + <option value="cadd.mirsvr.aln" selected="false">cadd.mirsvr.aln</option> + <option value="cadd.mirsvr.e" selected="false">cadd.mirsvr.e</option> + <option value="cadd.mirsvr.score" selected="false">cadd.mirsvr.score</option> + <option value="cadd.motif" selected="false">cadd.motif</option> + <option value="cadd.motif.dist" selected="false">cadd.motif.dist</option> + <option value="cadd.motif.ecount" selected="false">cadd.motif.ecount</option> + <option value="cadd.motif.ehipos" selected="false">cadd.motif.ehipos</option> + <option value="cadd.motif.ename" selected="false">cadd.motif.ename</option> + <option value="cadd.motif.escorechng" selected="false">cadd.motif.escorechng</option> + <option value="cadd.motif.toverlap" selected="false">cadd.motif.toverlap</option> + <option value="cadd.mutindex" selected="false">cadd.mutindex</option> + <option value="cadd.naa" selected="false">cadd.naa</option> + <option value="cadd.oaa" selected="false">cadd.oaa</option> + <option value="cadd.phast_cons" selected="false">cadd.phast_cons</option> + <option value="cadd.phast_cons.mammalian" selected="false">cadd.phast_cons.mammalian</option> + <option value="cadd.phast_cons.primate" selected="false">cadd.phast_cons.primate</option> + <option value="cadd.phast_cons.vertebrate" selected="false">cadd.phast_cons.vertebrate</option> + <option value="cadd.phred" selected="false">cadd.phred</option> + <option value="cadd.phylop" selected="false">cadd.phylop</option> + <option value="cadd.phylop.mammalian" selected="false">cadd.phylop.mammalian</option> + <option value="cadd.phylop.primate" selected="false">cadd.phylop.primate</option> + <option value="cadd.phylop.vertebrate" selected="false">cadd.phylop.vertebrate</option> + <option value="cadd.polyphen" selected="false">cadd.polyphen</option> + <option value="cadd.polyphen.cat" selected="false">cadd.polyphen.cat</option> + <option value="cadd.polyphen.val" selected="false">cadd.polyphen.val</option> + <option value="cadd.pos" selected="false">cadd.pos</option> + <option value="cadd.rawscore" selected="false">cadd.rawscore</option> + <option value="cadd.ref" selected="false">cadd.ref</option> + <option value="cadd.scoresegdup" selected="false">cadd.scoresegdup</option> + <option value="cadd.segway" selected="false">cadd.segway</option> + <option value="cadd.sift" selected="false">cadd.sift</option> + <option value="cadd.sift.cat" selected="false">cadd.sift.cat</option> + <option value="cadd.sift.val" selected="false">cadd.sift.val</option> + <option value="cadd.targetscans" selected="false">cadd.targetscans</option> + <option value="cadd.tf" selected="false">cadd.tf</option> + <option value="cadd.tf.bs" selected="false">cadd.tf.bs</option> + <option value="cadd.tf.bs_peaks" selected="false">cadd.tf.bs_peaks</option> + <option value="cadd.tf.bs_peaks_max" selected="false">cadd.tf.bs_peaks_max</option> + <option value="cadd.type" selected="false">cadd.type</option> + <option value="cgi" selected="false">cgi</option> + <option value="cgi.association" selected="false">cgi.association</option> + <option value="cgi.cdna" selected="false">cgi.cdna</option> + <option value="cgi.drug" selected="false">cgi.drug</option> + <option value="cgi.evidence_level" selected="false">cgi.evidence_level</option> + <option value="cgi.gene" selected="false">cgi.gene</option> + <option value="cgi.primary_tumor_type" selected="false">cgi.primary_tumor_type</option> + <option value="cgi.protein_change" selected="false">cgi.protein_change</option> + <option value="cgi.region" selected="false">cgi.region</option> + <option value="cgi.source" selected="false">cgi.source</option> + <option value="cgi.transcript" selected="false">cgi.transcript</option> + <option value="chrom" selected="false">chrom</option> + <option value="civic" selected="false">civic</option> + <option value="civic.clinvar_entries" selected="false">civic.clinvar_entries</option> + <option value="civic.coordinates" selected="false">civic.coordinates</option> + <option value="civic.coordinates.chromosome" selected="false">civic.coordinates.chromosome</option> + <option value="civic.coordinates.chromosome2" selected="false">civic.coordinates.chromosome2</option> + <option value="civic.coordinates.ensembl_version" selected="false">civic.coordinates.ensembl_version</option> + <option value="civic.coordinates.reference_bases" 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selected="false">grasp.discovery.east_asian</option> + <option value="grasp.discovery.european" selected="false">grasp.discovery.european</option> + <option value="grasp.discovery.filipino" selected="false">grasp.discovery.filipino</option> + <option value="grasp.discovery.hispanic" selected="false">grasp.discovery.hispanic</option> + <option value="grasp.discovery.indian_south_asian" selected="false">grasp.discovery.indian_south_asian</option> + <option value="grasp.discovery.indonesian" selected="false">grasp.discovery.indonesian</option> + <option value="grasp.discovery.micronesian" selected="false">grasp.discovery.micronesian</option> + <option value="grasp.discovery.mixed" selected="false">grasp.discovery.mixed</option> + <option value="grasp.discovery.native" selected="false">grasp.discovery.native</option> + <option value="grasp.discovery.total_samples" selected="false">grasp.discovery.total_samples</option> + <option value="grasp.discovery.unspecified" selected="false">grasp.discovery.unspecified</option> + <option value="grasp.eqtl_meth_metab_study" selected="false">grasp.eqtl_meth_metab_study</option> + <option value="grasp.exclusively_male_female" selected="false">grasp.exclusively_male_female</option> + <option value="grasp.gwas_ancestry_description" selected="false">grasp.gwas_ancestry_description</option> + <option value="grasp.hg19" selected="false">grasp.hg19</option> + <option value="grasp.hg19.chr" selected="false">grasp.hg19.chr</option> + <option value="grasp.hg19.pos" selected="false">grasp.hg19.pos</option> + <option value="grasp.hugfield" selected="false">grasp.hugfield</option> + <option value="grasp.human_enhancer" selected="false">grasp.human_enhancer</option> + <option value="grasp.in_gene" selected="false">grasp.in_gene</option> + <option value="grasp.in_mirna" selected="false">grasp.in_mirna</option> + <option value="grasp.in_mirna_bs" selected="false">grasp.in_mirna_bs</option> + <option value="grasp.includes_male_female_only_analyses" selected="false"> + grasp.includes_male_female_only_analyses + </option> + <option value="grasp.initial_sample_description" selected="false">grasp.initial_sample_description</option> + <option value="grasp.nearest_gene" selected="false">grasp.nearest_gene</option> + <option value="grasp.oreg_anno" selected="false">grasp.oreg_anno</option> + <option value="grasp.platform_snps_passing_qc" selected="false">grasp.platform_snps_passing_qc</option> + <option value="grasp.polyphen2" selected="false">grasp.polyphen2</option> + <option value="grasp.publication" selected="false">grasp.publication</option> + <option value="grasp.publication.journal" selected="false">grasp.publication.journal</option> + <option value="grasp.publication.location_within_paper" selected="false"> + grasp.publication.location_within_paper + </option> + <option value="grasp.publication.p_value" selected="false">grasp.publication.p_value</option> + <option value="grasp.publication.paper_phenotype_categories" selected="false"> + grasp.publication.paper_phenotype_categories + </option> + <option value="grasp.publication.paper_phenotype_description" selected="false"> + grasp.publication.paper_phenotype_description + </option> + <option value="grasp.publication.phenotype" selected="false">grasp.publication.phenotype</option> + <option value="grasp.publication.pmid" selected="false">grasp.publication.pmid</option> + <option value="grasp.publication.snpid" selected="false">grasp.publication.snpid</option> + <option value="grasp.publication.title" selected="false">grasp.publication.title</option> + <option value="grasp.replication" selected="false">grasp.replication</option> + <option value="grasp.replication.african" selected="false">grasp.replication.african</option> + <option value="grasp.replication.arab_me" selected="false">grasp.replication.arab_me</option> + <option value="grasp.replication.east_asian" selected="false">grasp.replication.east_asian</option> + <option value="grasp.replication.european" selected="false">grasp.replication.european</option> + <option value="grasp.replication.filipino" selected="false">grasp.replication.filipino</option> + <option value="grasp.replication.hispanic" selected="false">grasp.replication.hispanic</option> + <option value="grasp.replication.indian_south_asian" selected="false">grasp.replication.indian_south_asian + </option> + <option value="grasp.replication.indonesian" selected="false">grasp.replication.indonesian</option> + <option value="grasp.replication.micronesian" selected="false">grasp.replication.micronesian</option> + <option value="grasp.replication.mixed" selected="false">grasp.replication.mixed</option> + <option value="grasp.replication.native" selected="false">grasp.replication.native</option> + <option value="grasp.replication.total_samples" selected="false">grasp.replication.total_samples</option> + <option value="grasp.replication.unspecified" selected="false">grasp.replication.unspecified</option> + <option value="grasp.replication_sample_description" selected="false">grasp.replication_sample_description + </option> + <option value="grasp.rna_edit" selected="false">grasp.rna_edit</option> + <option value="grasp.sift" selected="false">grasp.sift</option> + <option value="grasp.srsid" selected="false">grasp.srsid</option> + <option value="grasp.uniprot" selected="false">grasp.uniprot</option> + <option value="gwassnps" selected="false">gwassnps</option> + <option value="gwassnps.genename" selected="false">gwassnps.genename</option> + <option value="gwassnps.pubmed" selected="false">gwassnps.pubmed</option> + <option value="gwassnps.pvalue" selected="false">gwassnps.pvalue</option> + <option value="gwassnps.pvalue_desc" selected="false">gwassnps.pvalue_desc</option> + <option value="gwassnps.region" selected="false">gwassnps.region</option> + <option value="gwassnps.risk_allele" selected="false">gwassnps.risk_allele</option> + <option value="gwassnps.risk_allele_freq" selected="false">gwassnps.risk_allele_freq</option> + <option value="gwassnps.rsid" selected="false">gwassnps.rsid</option> + <option value="gwassnps.title" selected="false">gwassnps.title</option> + <option value="gwassnps.trait" selected="false">gwassnps.trait</option> + <option value="hg19" selected="false">hg19</option> + <option value="hg19.end" selected="false">hg19.end</option> + <option value="hg19.start" selected="false">hg19.start</option> + <option value="mutdb" selected="false">mutdb</option> + <option value="mutdb.alt" selected="false">mutdb.alt</option> + <option value="mutdb.chrom" selected="false">mutdb.chrom</option> + <option value="mutdb.cosmic_id" selected="false">mutdb.cosmic_id</option> + <option value="mutdb.hg19" selected="false">mutdb.hg19</option> + <option value="mutdb.hg19.end" selected="false">mutdb.hg19.end</option> + <option value="mutdb.hg19.start" selected="false">mutdb.hg19.start</option> + <option value="mutdb.mutpred_score" selected="false">mutdb.mutpred_score</option> + <option value="mutdb.ref" selected="false">mutdb.ref</option> + <option value="mutdb.rsid" selected="false">mutdb.rsid</option> + <option value="mutdb.strand" selected="false">mutdb.strand</option> + <option value="mutdb.uniprot_id" selected="false">mutdb.uniprot_id</option> + <option value="observed" selected="false">observed</option> + <option value="snpedia" selected="false">snpedia</option> + <option value="snpedia.text" selected="false">snpedia.text</option> + <option value="snpeff" selected="false">snpeff</option> + <option value="snpeff.ann" selected="false">snpeff.ann</option> + <option value="snpeff.ann.cdna" selected="false">snpeff.ann.cdna</option> + <option value="snpeff.ann.cdna.length" selected="false">snpeff.ann.cdna.length</option> + <option value="snpeff.ann.cdna.position" selected="false">snpeff.ann.cdna.position</option> + <option value="snpeff.ann.cds" selected="false">snpeff.ann.cds</option> + <option value="snpeff.ann.cds.length" selected="false">snpeff.ann.cds.length</option> + <option value="snpeff.ann.cds.position" selected="false">snpeff.ann.cds.position</option> + <option value="snpeff.ann.distance_to_feature" selected="false">snpeff.ann.distance_to_feature</option> + <option value="snpeff.ann.effect" selected="false">snpeff.ann.effect</option> + <option value="snpeff.ann.feature_id" selected="false">snpeff.ann.feature_id</option> + <option value="snpeff.ann.feature_type" selected="false">snpeff.ann.feature_type</option> + <option value="snpeff.ann.gene_id" selected="false">snpeff.ann.gene_id</option> + <option value="snpeff.ann.genename" selected="false">snpeff.ann.genename</option> + <option value="snpeff.ann.hgvs_c" selected="false">snpeff.ann.hgvs_c</option> + <option value="snpeff.ann.hgvs_p" selected="false">snpeff.ann.hgvs_p</option> + <option value="snpeff.ann.protein" selected="false">snpeff.ann.protein</option> + <option value="snpeff.ann.protein.length" selected="false">snpeff.ann.protein.length</option> + <option value="snpeff.ann.protein.position" selected="false">snpeff.ann.protein.position</option> + <option value="snpeff.ann.putative_impact" selected="false">snpeff.ann.putative_impact</option> + <option value="snpeff.ann.rank" selected="false">snpeff.ann.rank</option> + <option value="snpeff.ann.total" selected="false">snpeff.ann.total</option> + <option value="snpeff.ann.transcript_biotype" selected="false">snpeff.ann.transcript_biotype</option> + <option value="snpeff.lof" selected="false">snpeff.lof</option> + <option value="snpeff.lof.gene_id" selected="false">snpeff.lof.gene_id</option> + <option value="snpeff.lof.genename" selected="false">snpeff.lof.genename</option> + <option value="snpeff.lof.number_of_transcripts_in_gene" selected="false"> + snpeff.lof.number_of_transcripts_in_gene + </option> + <option value="snpeff.lof.percent_of_transcripts_affected" selected="false"> + snpeff.lof.percent_of_transcripts_affected + </option> + <option value="snpeff.nmd" selected="false">snpeff.nmd</option> + <option value="snpeff.nmd.gene_id" selected="false">snpeff.nmd.gene_id</option> + <option value="snpeff.nmd.genename" selected="false">snpeff.nmd.genename</option> + <option value="snpeff.nmd.number_of_transcripts_in_gene" selected="false"> + snpeff.nmd.number_of_transcripts_in_gene + </option> + <option value="snpeff.nmd.percent_of_transcripts_affected" selected="false"> + snpeff.nmd.percent_of_transcripts_affected + </option> + <option value="vcf" selected="false">vcf</option> + <option value="vcf.alt" selected="false">vcf.alt</option> + <option value="vcf.position" selected="false">vcf.position</option> + <option value="vcf.ref" selected="false">vcf.ref</option> + <option value="wellderly" selected="false">wellderly</option> + <option value="wellderly.alt" selected="false">wellderly.alt</option> + <option value="wellderly.chrom" selected="false">wellderly.chrom</option> + <option value="wellderly.coding_impact" selected="false">wellderly.coding_impact</option> + <option value="wellderly.gene" selected="false">wellderly.gene</option> + <option value="wellderly.hg19" selected="false">wellderly.hg19</option> + <option value="wellderly.hg19.end" selected="false">wellderly.hg19.end</option> + <option value="wellderly.hg19.start" selected="false">wellderly.hg19.start</option> + <option value="wellderly.polyphen" selected="false">wellderly.polyphen</option> + <option value="wellderly.pos" selected="false">wellderly.pos</option> + <option value="wellderly.ref" selected="false">wellderly.ref</option> + <option value="wellderly.sift" selected="false">wellderly.sift</option> + <option value="wellderly.vartype" selected="false">wellderly.vartype</option> + </xml> +</macros> \ No newline at end of file
--- a/variant_simple_search.Rmd Tue Mar 20 11:29:28 2018 -0400 +++ b/variant_simple_search.Rmd Tue Mar 20 13:59:04 2018 -0400 @@ -19,12 +19,9 @@ # Code for computational analysis -```{r 'step 1'} - -``` - -```{r 'ste[ 2'} - +```{r} +opt ``` +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_simple_search.csv Tue Mar 20 13:59:04 2018 -0400 @@ -0,0 +1,6 @@ +short flag,argument mask,data type,variable name,galaxy input type,description +o,1,character,report,data, +d,1,character,report.files_path,data, +s,1,character,sink_message,text, +q,1,character,variant_query,text, +f,1,character,return_fields,text,
--- a/variant_simple_search.xml Tue Mar 20 11:29:28 2018 -0400 +++ b/variant_simple_search.xml Tue Mar 20 13:59:04 2018 -0400 @@ -1,30 +1,54 @@ -<tool name="Tool report" id="tool_1" version="1.0.0"> - <description> +<tool id="tool_1" name="variant_simple_search" version="1.0.0"> + <description> some description </description> - <requirements> - <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="1.5">r-jsonlite</requirement><requirement type="package" version="0.2">r-dt</requirement><requirement type="package" version="3.1">r-curl</requirement><requirement type="package" version="1.95_4.8">r-rcurl</requirement></requirements> - <stdio> - <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio> - <command><![CDATA[ - export TOOL_DIRECTORY='${__tool_directory__}' && + <requirements> + <requirement type="package" version="1.15.0.6-0">pandoc</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.6">r-rmarkdown</requirement> + <requirement type="package" version="1.5">r-jsonlite</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="3.1">r-curl</requirement> + <requirement type="package" version="1.95_4.8">r-rcurl</requirement> + </requirements> + <macros> + <import>mygene_and_myvariant_macros.xml</import> + </macros> + <stdio> + <regex match="XXX" source="stderr" level="warning" + description="Check the warnings_and_errors.txt file for more details."/> + </stdio> + <command><![CDATA[ + export TOOL_DIR='${__tool_directory__}' && - Rscript '${__tool_directory__}/rmarkdown_report_render.R' + Rscript '${__tool_directory__}/variant_simple_search_render.R' - -e $echo -o $report -d $report.files_path -s $sink_message - -t '${__tool_directory__}' + -q $variant_query + -f $return_fields ]]></command> - <inputs> - <param type="select" name="return_fields" label="Returned fields" optional="False" multiple="True"><option value="field1" selected="false">field1</option></param></inputs> - <outputs> - <data format="html" name="report" label="tool report"/><data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/></outputs> - <citations> + <inputs> + <param type="text" name="variant_query" label="Search keywords" optional="False"> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + </valid> + </sanitizer> + </param> + <param type="select" name="return_fields" label="Returned fields" optional="False" multiple="True"> + <expand macro="fields" /> + </param> + </inputs> + <outputs> + <data format="html" name="report" label="${tool.name} report"/> + <data format="txt" name="sink_message" label="${tool.name} log" from_work_dir="warnings_and_errors.txt"/> + </outputs> + <citations> <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown, title={rmarkdown: Dynamic Documents for R, 2016}, @@ -34,7 +58,8 @@ volume={6}, year={2016} } - ]]></citation><citation type="bibtex"><![CDATA[ + ]]></citation> + <citation type="bibtex"><![CDATA[ @book{xie2015dynamic, title={Dynamic Documents with R and knitr}, author={Xie, Yihui}, @@ -42,5 +67,6 @@ year={2015}, publisher={CRC Press} } - ]]></citation></citations> + ]]></citation> + </citations> </tool>
--- a/variant_simple_search_render.R Tue Mar 20 11:29:28 2018 -0400 +++ b/variant_simple_search_render.R Tue Mar 20 13:59:04 2018 -0400 @@ -10,6 +10,8 @@ library(getopt) library(rmarkdown) +library(jsonlite) +library(DT) #------------------------------------------------ @@ -17,11 +19,11 @@ # load helper function source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R')) # import getopt specification matrix from a csv file -spec_csv = paste0(Sys.getenv('TOOL_DIR'), '/getopt_specification.csv') -opt = getopt(getopt_specification_matrix(spec_csv)) +opt = getopt(getopt_specification_matrix('/variant_simple_search.csv')) opt$X_t = Sys.getenv('TOOL_DIR') #---------------------------------------------------- +print(opt) #-----------using passed arguments in R # to define system environment variables--- @@ -34,7 +36,7 @@ OUTPUT_DIR = opt$X_d TOOL_DIR = opt$X_t OUTPUT_REPORT = opt$X_o -RMD_NAME = '' +RMD_NAME = 'variant_simple_search.Rmd' # create the output associated directory to store all outputs dir.create(OUTPUT_DIR, recursive = TRUE)