| Next changeset 1:e9758eee6697 (2015-04-28) |
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COPYING kggseq_variant_selection.xml tool_dependencies.xml |
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| diff -r 000000000000 -r d388273fb83f COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 12 21:40:16 2014 -0400 |
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| @@ -0,0 +1,23 @@ +Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ +Created by: +Paolo Uva <paolo.uva@crs4.it> +Nicola Soranzo <nicola.soranzo@crs4.it> + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. +IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, +TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
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| diff -r 000000000000 -r d388273fb83f kggseq_variant_selection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kggseq_variant_selection.xml Fri Sep 12 21:40:16 2014 -0400 |
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| b'@@ -0,0 +1,407 @@\n+<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.1">\n+ <description></description>\n+ <requirements>\n+ <requirement type="package" version="0.4_20140910">kggseq</requirement>\n+ </requirements>\n+ <command>\n+java -jar \\$KGGSEQ_JAR_PATH/kggseq.jar\n+## Environmental settings\n+--buildver hg19\n+--resource \\$KGGSEQ_JAR_PATH/resources\n+--no-lib-check\n+--no-resource-check\n+--no-progress-check\n+--out results\n+--o-vcf\n+\n+--vcf-file $inputFile\n+--ped-file $pedFile\n+--db-gene $db_gene\n+$composite_subject_id\n+\n+## Variant filters\n+$pass_variant_only\n+#if str($variant_filters.variant_filters_select) == "yes"\n+ --seq-qual $variant_filters.seq_qual\n+ --seq-mq $variant_filters.seq_mq\n+ --seq-sb $variant_filters.seq_sb\n+ --seq-fs $variant_filters.seq_fs\n+ --min-heta $variant_filters.min_heta\n+ --min-homa $variant_filters.min_homa\n+ --min-hetu $variant_filters.min_hetu\n+ --min-homu $variant_filters.min_homu\n+ --min-obsa $variant_filters.min_obsa\n+ --min-obsu $variant_filters.min_obsu\n+ --min-obs $variant_filters.min_obs\n+ #if str($variant_filters.hwe_control)\n+ --hwe-control $variant_filters.hwe_control\n+ #end if\n+ #if str($variant_filters.hwe_case)\n+ --hwe-case $variant_filters.hwe_case\n+ #end if\n+ #if str($variant_filters.hwe_all)\n+ --hwe-all $variant_filters.hwe_all\n+ #end if\n+#else\n+ --seq-qual 0\n+ --seq-mq 0\n+#end if\n+\n+## Genotype filters\n+#if str($genotype_filters.genotype_filters_select) == "yes"\n+ --gty-qual $genotype_filters.gty_qual\n+ --gty-dp $genotype_filters.gty_dp\n+ --gty-sec-pl $genotype_filters.gty_sec_pl\n+ --gty-af-ref $genotype_filters.gty_af_ref\n+ --gty-af-het $genotype_filters.gty_af_het\n+ --gty-af-alt $genotype_filters.gty_af_alt\n+#else\n+ --gty-qual 0\n+ --gty-dp 0\n+ --gty-sec-pl 0\n+ --gty-af-ref 1\n+ --gty-af-het 0\n+ --gty-af-alt 0\n+#end if\n+\n+## Genetic inheritance\n+#if str($genetic_filters.genetic_filters_select) == "yes"\n+ #if str($genetic_filters.genetic_model.genetic_model_select) == "yes"\n+ #if $genetic_filters.genetic_model.custom_genetic_params\n+ --genotype-filter $genetic_filters.genetic_model.custom_genetic_params\n+ #end if\n+ #else\n+ $genetic_filters.genetic_model.suggested_genetic_params\n+ #end if\n+#end if\n+\n+## Gene feature filters\n+#if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features\n+ --gene-feature-in $gene_feature_filters.gene_features\n+ --splicing $gene_feature_filters.splicing\n+ --neargene $gene_feature_filters.neargene\n+#end if\n+\n+## Common variants filters\n+#if str($allele_freq_filters.allele_freq_filters_select) == "yes"\n+ #if $allele_freq_filters.allele_freq_db\n+ --db-filter $allele_freq_filters.allele_freq_db\n+ #end if\n+ --rare-allele-freq $allele_freq_filters.rare_allele_freq\n+#end if\n+\n+## Genomic regions filters\n+#if str($genomic_region_filters.genomic_region_filters_select) == "yes"\n+ $genomic_region_filters.ignore_indel_or_snv\n+ #if $genomic_region_filters.regions_in\n+ --regions-in "$genomic_region_filters.regions_in"\n+ #end if\n+ #if $genomic_region_filters.regions_out\n+ --regions-out "$genomic_region_filters.regions_out"\n+ #end if\n+ #if $genomic_region_filters.genes_in\n+ --genes-in "$genomic_region_filters.genes_in"\n+ #end if\n+ #if $genomic_region_filters.genes_out\n+ --genes-out "$genomic_region_filters.genes_out"\n+ #end if\n+ $genomic_region_filters.superdup\n+ #if str($genomic_region_filters.gene_var_filter)\n+ --gene-var-filter $genomic_region_filters.gene_var_filter\n+ #end if\n+#end if\n+\n+## Predicted impact filters\n+#if str($impact_filters.impact_filters_select) == "yes"\n+ --db-score dbnsfp\n+ $impact_filters.filter_nondisease_variant\n+ $impact_filters.mendel_causing\n+#end if\n+\n+## Add annotations\n+#if str($add_annotations.add_annotations_select) == "yes"\n+ $add_annotations.genome_annotation\n+ $add_annotations.omim_annotation\n+ $add_annotations.cosmic_annotation\n+ #if $add_annotations.'..b'\n+ <option value="cano">Canonical pathways (1452)</option>\n+ <option value="onco">Oncogenic signatures (189)</option>\n+ <option value="cmop">Computational gene sets (858)</option>\n+ <option value="onto">Gene Ontology gene sets (1454)</option>\n+ </param>\n+ </when>\n+ <when value="no" />\n+ </conditional>\n+ </when>\n+ <when value="no" />\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="outVcf" format="vcf" label="${tool.name} on ${on_string}: VCF" from_work_dir="results.flt.vcf" />\n+ <data name="outTabular" format="tabular" label="${tool.name} on ${on_string}: tabular" from_work_dir="results.flt.txt" />\n+ <data name="outDoubleHitTriosGty" format="tabular" label="${tool.name} on ${on_string}: double-hit genotypes" from_work_dir="results.doublehit.gene.trios.flt.gty.txt">\n+ <filter>genetic_filters[\'genetic_filters_select\'] == "yes" and genetic_filters[\'genetic_model\'][\'genetic_model_select\'] == "no" and genetic_filters[\'genetic_model\'][\'suggested_genetic_params\'] == "--double-hit-gene-trio-filter"</filter>\n+ </data>\n+ <data name="outDoubleHitTriosCount" format="tabular" label="${tool.name} on ${on_string}: double-hit counts" from_work_dir="results.doublehit.gene.trios.flt.count.txt">\n+ <filter>genetic_filters[\'genetic_filters_select\'] == "yes" and genetic_filters[\'genetic_model\'][\'genetic_model_select\'] == "no" and genetic_filters[\'genetic_model\'][\'suggested_genetic_params\'] == "--double-hit-gene-trio-filter"</filter>\n+ </data>\n+ <data name="outDoubleHitPhasedGty" format="tabular" label="${tool.name} on ${on_string}: double-hit phased genotypes" from_work_dir="results.doublehit.gene.phased.flt.gty.txt">\n+ <filter>genetic_filters[\'genetic_filters_select\'] == "yes" and genetic_filters[\'genetic_model\'][\'genetic_model_select\'] == "no" and genetic_filters[\'genetic_model\'][\'suggested_genetic_params\'] == "--double-hit-gene-phased-filter"</filter>\n+ </data>\n+ <data name="outDoubleHitPhasedCount" format="tabular" label="${tool.name} on ${on_string}: double-hit phased counts" from_work_dir="results.doublehit.gene.phased.flt.count.txt">\n+ <filter>genetic_filters[\'genetic_filters_select\'] == "yes" and genetic_filters[\'genetic_model\'][\'genetic_model_select\'] == "no" and genetic_filters[\'genetic_model\'][\'suggested_genetic_params\'] == "--double-hit-gene-phased-filter"</filter>\n+ </data>\n+ <data name="logFile" format="txt" label="${tool.name} on ${on_string}: log" />\n+ </outputs>\n+ <help>\n+**What it does**\n+\n+This tool uses `KGGSeq`_ to filter and prioritize genetic variants from sequencing data.\n+\n+**License and citation**\n+\n+This Galaxy tool is Copyright \xc2\xa9 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.\n+\n+.. _CRS4 Srl.: http://www.crs4.it/\n+.. _MIT license: http://opensource.org/licenses/MIT\n+\n+You can use this tool only if you agree to the license terms of: `KGGSeq`_.\n+\n+.. _KGGSeq: http://statgenpro.psychiatry.hku.hk/limx/kggseq/\n+\n+If you use this tool, please cite:\n+\n+- |Cuccuru2014|_\n+- |Li2012|_\n+- |Li2013|_.\n+\n+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929\n+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928\n+.. |Li2012| replace:: Li, M.-X., *et al.* (2012) A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. *Nucleic Acids Res.* 40(7), e53\n+.. _Li2012: http://nar.oxfordjournals.org/content/40/7/e53\n+.. |Li2013| replace:: Li, M.-X., *et al.* (2013) Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies. *PLoS Genet.* 9(1), e1003143\n+.. _Li2013: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003143\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r d388273fb83f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 12 21:40:16 2014 -0400 |
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| @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="kggseq" version="0.4_20140910"> + <install version="1.0"> + <actions> + <action type="download_by_url" target_filename="kggseq_archive-0.4_20140910.tar.gz">https://github.com/nsoranzo/kggseq_archive/archive/v0.4_20140910.tar.gz</action> + <action type="shell_command">touch test.vcf</action> + <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter hg19_1kg201305,hg19_1kg201204,hg19_ESP6500AA,hg19_ESP6500EA,hg19_dbsnp141,hg19_dbsnp138,hg19_dbsnp137 --genome-annot --db-gene refgene,gencode,knowngene --db-score dbnsfp --superdup-annot --vcf-file test.vcf</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |