| Previous changeset 5:675fa55f5c02 (2016-01-08) Next changeset 8:2f40467536cf (2016-04-09) |
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Commit message:
Update help |
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modified:
snpSift_annotate.xml snpSift_extractFields.xml snpSift_filter.xml tool_dependencies.xml |
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| diff -r 675fa55f5c02 -r c29f29a6f26c snpSift_annotate.xml --- a/snpSift_annotate.xml Fri Jan 08 08:28:51 2016 -0600 +++ b/snpSift_annotate.xml Mon Jan 25 17:02:52 2016 -0600 |
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| @@ -27,7 +27,7 @@ <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> <when value="id"/> <when value="info"> - <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" + <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" help="list is a comma separated list of fields. When blank, all INFO fields are included"> <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> |
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| diff -r 675fa55f5c02 -r c29f29a6f26c snpSift_extractFields.xml --- a/snpSift_extractFields.xml Fri Jan 08 08:28:51 2016 -0600 +++ b/snpSift_extractFields.xml Mon Jan 25 17:02:52 2016 -0600 |
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| @@ -26,11 +26,11 @@ </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> - <param name="extract" type="text" label="Extract" size="160" help="Need help? See below a few examples." /> + <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." /> <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" /> - <param name="separator" type="text" value="" optional="true" label="multiple field separator" size="1" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values"> + <param name="separator" type="text" value="" optional="true" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values"> </param> - <param name="empty_text" type="text" value="" optional="true" label="empty field text" size="10" help="Represent empty fields with this value, rather than leaving them blank" > + <param name="empty_text" type="text" value="" optional="true" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" > </param> </inputs> <outputs> @@ -88,13 +88,13 @@ SnpEff 'ANN' fields: "ANN[*].ALLELE" (alias GENOTYPE) "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.) - "ANN[*].IMPACT:" { HIGH, MODERATE, LOW, MODIFIER } - "ANN[*].GENE:" Gene name (e.g. 'PSD3') - "ANN[*].GENEID:" Gene ID - "ANN[*].FEATURE - " ANN[*].FEATUREID (alias TRID: Transcript ID) - "ANN[*].BIOTYPE:" Biotype, as described by the annotations (e.g. 'protein_coding') - "ANN[*].RANK:" Exon or Intron rank (i.e. exon number in a transcript) + "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER } + "ANN[*].GENE" Gene name (e.g. 'PSD3') + "ANN[*].GENEID" Gene ID + "ANN[*].FEATURE" + "ANN[*].FEATUREID" (alias TRID: Transcript ID) + "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding') + "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript) "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation "ANN[*].CDNA_POS" (alias POS_CDNA) |
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| diff -r 675fa55f5c02 -r c29f29a6f26c snpSift_filter.xml --- a/snpSift_filter.xml Fri Jan 08 08:28:51 2016 -0600 +++ b/snpSift_filter.xml Mon Jan 25 17:02:52 2016 -0600 |
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| @@ -28,7 +28,7 @@ </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> - <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." /> + <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." /> <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" /> <conditional name="filtering"> <param name="mode" type="select" label="Filter mode"> @@ -42,12 +42,12 @@ help="appends an ID tag to non-matching entry FILTER "/> <when value="no"/> <when value="yes"> - <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10" + <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." help="Default ID is 'SnpSift'"/> </when> </conditional> - <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/> - <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/> + <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." /> + <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." /> </when> </conditional> </inputs> @@ -87,7 +87,7 @@ <test> <param name="input" ftype="vcf" value="test01.vcf"/> - <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> + <param name="expr" value="(POS >= 20175) & (POS < 35549)"/> <param name="mode" value="entries"/> <output name="output"> <assert_contents> |
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| diff -r 675fa55f5c02 -r c29f29a6f26c tool_dependencies.xml --- a/tool_dependencies.xml Fri Jan 08 08:28:51 2016 -0600 +++ b/tool_dependencies.xml Mon Jan 25 17:02:52 2016 -0600 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="snpEff" version="4.1"> - <repository changeset_revision="02a5e07a4121" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="625bc8f7929d" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |