diff snpSift_extractFields.xml @ 6:824f78c0d0df

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty

--- a/snpSift_extractFields.xml	Wed Dec 09 14:03:26 2015 -0500
+++ b/snpSift_extractFields.xml	Mon Jan 25 17:40:56 2016 -0500
@@ -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)