| Previous changeset 3:563d1bdb7b80 (2016-12-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 |
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modified:
snpSift_dbnsfp.xml snpSift_macros.xml |
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| diff -r 563d1bdb7b80 -r 4e21e4f2bc48 snpSift_dbnsfp.xml --- a/snpSift_dbnsfp.xml Mon Dec 19 11:57:06 2016 -0500 +++ b/snpSift_dbnsfp.xml Mon Jun 12 10:25:44 2017 -0400 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">\n- <description>Add Annotations from dbNSFP or similar annotation DBs</description>\n+<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">\n+ <description>Add annotations from dbNSFP or similar annotation DBs</description>\n <macros>\n <import>snpSift_macros.xml</import>\n </macros>\n@@ -7,23 +7,21 @@\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command><![CDATA[\n- @CONDA_SNPSIFT_JAR_PATH@ &&\n- java -Xmx6G -jar "\\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v\n- #if $db.dbsrc == \'cached\':\n- -db "$db.dbnsfp"\n- #if $db.annotations and str($db.annotations) != \'\':\n- -f "$db.annotations"\n- #end if\n- #else:\n- -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"\n- #if $db.annotations and str($db.annotations) != \'\':\n- -f "$db.annotations"\n- #end if\n- #end if\n- "$input" > "$output"\n- 2> tmp.err && grep -v file tmp.err\n-]]>\n- </command>\n+SnpSift -Xmx6G dbnsfp -v\n+#if $db.dbsrc == \'cached\':\n+ -db \'$db.dbnsfp\'\n+ #if $db.annotations and str($db.annotations) != \'\':\n+ -f \'$db.annotations\'\n+ #end if\n+#else:\n+ -db \'${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}\'\n+ #if $db.annotations and str($db.annotations) != \'\':\n+ -f \'$db.annotations\'\n+ #end if\n+#end if\n+\'$input\' > \'$output\'\n+2> tmp.err && grep -v file tmp.err\n+ ]]></command>\n <inputs>\n <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>\n <conditional name="db">\n@@ -50,15 +48,15 @@\n <when value="history">\n <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>\n <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">\n- <options>\n- <filter type="data_meta" ref="dbnsfpdb" key="annotation" />\n- </options>\n+ <options>\n+ <filter type="data_meta" ref="dbnsfpdb" key="annotation" />\n+ </options>\n </param>\n </when>\n </conditional>\n </inputs>\n <outputs>\n- <data format="vcf" name="output" />\n+ <data name="output" format="vcf" />\n </outputs>\n <tests>\n <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular\n@@ -78,220 +76,211 @@\n </test> -->\n </tests>\n <help><![CDATA[\n-\n The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).\n It contains variant annotations such as:\n \n-\n- 1000Gp1_AC\n+1000Gp1_AC\n Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data\n- 1000Gp1_AF\n+1000Gp1_AF\n Alternative allele frequency in the whole 1000Gp1 data\n- 1000Gp1_AFR_AC\n+1000Gp1_AFR_AC\n Alternative allele counts in the 1000Gp1 African descendent samples\n- 1000Gp1_AFR_AF\n+1000Gp1_AFR_AF\n Alternative allele frequency in the 1000Gp1 African descendent samples\n- 1000Gp1_AMR_AC\n+1000Gp1_AMR_AC\n Alternative allele counts in the 1000Gp1 American descendent samples\n- 1000Gp1_AMR_AF\n+1000Gp1_AMR_AF\n Alternative allele frequency in the 1000Gp1 American descendent samples\n- 1000Gp1_ASN_AC\n+1000Gp1_ASN_AC\n Alternative allele counts in the 1000Gp1 Asian descendent samples\n- 1000Gp1_ASN_AF\n+1000Gp1_ASN_AF\n Alternative allele frequency in the 1000Gp1 Asian descendent samples\n- 1000Gp1_EUR_AC\n+1000Gp1_EUR_AC\n Alternative allele counts in the 1000Gp1 European descendent samples\n- 1000Gp1_EUR_AF\n+1000Gp1_EUR_AF\n Alternative allele frequency in the 1000Gp1 European descendent samples\n- aaalt\n+aaalt\n Alternative amino acid. "." if the variant is a spli'..b'ndicates negative selection, and a positive value indicates positive selection. Larger magnitude of the value suggests stronger evidence\n- Uniprot_aapos\n+Uniprot_aapos\n Amino acid position as to Uniprot. Multiple entries separated by ";"\n- Uniprot_acc\n+Uniprot_acc\n Uniprot accession number. Multiple entries separated by ";"\n- Uniprot_id\n+Uniprot_id\n Uniprot ID number. Multiple entries separated by ";"\n- UniSNP_ids\n+UniSNP_ids\n rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...\n \n-\n-The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds. \n+The dbNSFP database is available from https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds.\n \n-The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:\n-*( It also provides links for dbNSFP databases prebuilt for SnpSift )*\n+The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp and a couple of prebuilt dbNSFP databases are available at:\n http://snpeff.sourceforge.net/SnpSift.html#dbNSFP\n \n-However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::\n+However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:\n+\n+- The first line of the file must be column headers that name the annotations.\n+- The first 4 columns are required and must be:\n \n-\t- The first line of the file must be column headers that name the annotations. \n-\t- The first 4 columns are required and must be::\n-\t\t1. chromosome \n-\t\t2. position in chromosome\n-\t\t3. reference base\n-\t\t4. alternate base\n+ 1. chr: chromosome\n+ 2. pos(1-coor): position in chromosome\n+ 3. ref: reference base\n+ 4. alt: alternate base\n \n-For example:\n-\n-::\n+For example::\n \n-\t#chr\tpos(1-coor)\tref\talt\taaref\taaalt\tgenename\tSIFT_score\n-\t1\t69134\tA\tC\tE\tA\tOR4F5\t0.03\n-\t1\t69134\tA\tG\tE\tG\tOR4F5\t0.09\n-\t1\t69134\tA\tT\tE\tV\tOR4F5\t0.03\n-\t4\t100239319\tT\tA\tH\tL\tADH1B\t0\n-\t4\t100239319\tT\tC\tH\tR\tADH1B\t0.15\n-\t4\t100239319\tT\tG\tH\tP\tADH1B\t0\n+ #chr\tpos(1-coor)\tref\talt\taaref\taaalt\tgenename\tSIFT_score\n+ 1\t69134\tA\tC\tE\tA\tOR4F5\t0.03\n+ 1\t69134\tA\tG\tE\tG\tOR4F5\t0.09\n+ 1\t69134\tA\tT\tE\tV\tOR4F5\t0.03\n+ 4\t100239319\tT\tA\tH\tL\tADH1B\t0\n+ 4\t100239319\tT\tC\tH\tR\tADH1B\t0.15\n+ 4\t100239319\tT\tG\tH\tP\tADH1B\t0\n \n+The Galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:\n \n-The galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:\n- 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**\n- 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.\n-\n+1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**\n+2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.\n \n @EXTERNAL_DOCUMENTATION@\n-\thttp://snpeff.sourceforge.net/SnpSift.html#dbNSFP\n-]]>\n- </help>\n+- http://snpeff.sourceforge.net/SnpSift.html#dbNSFP\n+ ]]></help>\n <expand macro="citations">\n- <citation type="doi">DOI: 10.1002/humu.21517</citation>\n- <citation type="doi">DOI: 10.1002/humu.22376</citation>\n- <citation type="doi">DOI: 10.1002/humu.22932</citation>\n- <citation type="doi">doi: 10.1093/hmg/ddu733</citation>\n- <citation type="doi">doi: 10.1093/nar/gku1206</citation>\n- <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>\n+ <citation type="doi">10.1002/humu.21517</citation>\n+ <citation type="doi">10.1002/humu.22932</citation>\n+ <citation type="doi">10.1093/hmg/ddu733</citation>\n+ <citation type="doi">10.3389/fgene.2012.00035</citation>\n </expand>\n </tool>\n' |
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| diff -r 563d1bdb7b80 -r 4e21e4f2bc48 snpSift_macros.xml --- a/snpSift_macros.xml Mon Dec 19 11:57:06 2016 -0500 +++ b/snpSift_macros.xml Mon Jun 12 10:25:44 2017 -0400 |
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| @@ -1,33 +1,31 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.1">snpsift</requirement> + <requirement type="package" version="4.3.1p">snpsift</requirement> </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - </xml> - <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token> - <xml name="version_command"> - <version_command><![CDATA[ - if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && - java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1 - ]]></version_command> - </xml> - <token name="@WRAPPER_VERSION@">4.1</token> - <token name="@EXTERNAL_DOCUMENTATION@"> + <xml name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token> + <xml name="version_command"> + <version_command><![CDATA[ +SnpSift dbnsfp 2>&1|head -n 1 + ]]></version_command> + </xml> + <token name="@WRAPPER_VERSION@">4.3</token> + <token name="@EXTERNAL_DOCUMENTATION@"> +For details about this tool, please go to: -For details about this tool, please go to: - http://snpeff.sourceforge.net/SnpEff_manual.html - - </token> - <xml name="citations"> - <citations> - <citation type="doi">10.3389/fgene.2012.00035</citation> - <yield /> - </citations> - </xml> +- http://snpeff.sourceforge.net/SnpEff_manual.html + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.3389/fgene.2012.00035</citation> + <yield /> + </citations> + </xml> </macros> |