# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1453762972 21600
# Node ID c29f29a6f26c879e4930a03f11594bea02dd95de
# Parent  675fa55f5c02bdd5133887319af44c2e68b54609# Parent  824f78c0d0dfa59b294f1760a7dd94015cc290af
Update help

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
@@ -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>
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
@@ -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)
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
@@ -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) &amp; (POS &lt;= 35549)"/>
+        <param name="expr" value="(POS >= 20175) &amp; (POS &lt; 35549)"/>
         <param name="mode" value="entries"/>
         <output name="output">
             <assert_contents>
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
@@ -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>