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changeset 2:bf8c1526871b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:11:18 -0500
parents 98708b88af9f
children 20c7d583fec1
files snpSift_annotate.xml snpSift_caseControl.xml snpSift_extractFields.xml snpSift_filter.xml snpSift_int.xml snpSift_macros.xml snpSift_rmInfo.xml snpSift_vartype.xml snpSift_vcfCheck.xml tool_dependencies.xml
diffstat 10 files changed, 101 insertions(+), 123 deletions(-) [+]
line wrap: on
line diff
--- a/snpSift_annotate.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_annotate.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,6 +1,6 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1">
     <description>SNPs from dbSnp</description>
-    <!-- 
+    <!--
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
     <macros>
@@ -10,33 +10,33 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd
         #if $annotate.id :
           -id
         #elif str($annotate.info_ids).strip() != '' :
           -info "$annotate.info_ids"
-        #end if          
-        -q "$dbSnp" "$input" > "$output" 
+        #end if
+        -q "$dbSnp" "$input" > "$output"
 ]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
-        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
+        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
             help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
         <conditional name="annotate">
             <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
             <when value="id"/>
             <when value="info">
-                <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
-                    help="list is a comma separated list of fields. When blank, all INFO fields are included">    
+                <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
                     <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
                 </param>
             </when>
         </conditional>
-        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> 
+        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
             <help>
                 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
-                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 
+                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
             </help>
             </param>
     </inputs>
--- a/snpSift_caseControl.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_caseControl.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,6 +1,6 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1">
     <description>Count samples are in 'case' and 'control' groups.</description>
-    <!-- 
+    <!--
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
     <macros>
@@ -10,16 +10,17 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
-    #if str($name).strip() != '':
-      -name "$name"
-    #end if
-    #if $ctrl.ctrl_src == 'caseString':
-      '$ctrl.caseControlStr' 
-    #else
-      -tfam "$ctrl.tfam"
-    #end if
-    "$input" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q
+        #if str($name).strip() != '':
+            -name "$name"
+        #end if
+        #if $ctrl.ctrl_src == 'caseString':
+            '$ctrl.caseControlStr'
+        #else
+            -tfam "$ctrl.tfam"
+        #end if
+        "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -41,8 +42,8 @@
             <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
         </when>
         </conditional>
-        <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
-            <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
+        <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags">
+            <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
         </param>
     </inputs>
     <outputs>
@@ -90,13 +91,13 @@
 
 **SnpSift CaseControl**
 
-Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 
+Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
 
-Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 
+Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
 
 This command adds two annotations to the VCF file:
 
- - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 
+ - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
 
   "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
 
@@ -110,7 +111,7 @@
 
   - Hom/Het case = "hom"
 
-  - Hom/Het control = "any"  
+  - Hom/Het control = "any"
 
   - Case / Control column designation = ""++++------"
 
--- a/snpSift_extractFields.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_extractFields.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,6 +1,6 @@
-<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.1">
     <options sanitize="False" />
-    <description>from a VCF file inot a tabular file</description>
+    <description>from a VCF file into a tabular file</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
@@ -8,16 +8,17 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        @CONDA_SNPSIFT_JAR_PATH@ &&
         cat "$input"
         #if $one_effect_per_line:
-          | "\$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl"
-        #end if 
-        | java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" extractFields 
+          | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
+        #end if
+        | java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" extractFields
         #if $separator:
-          -s '$separator'  
+          -s '$separator'
         #end if
         #if $empty_text:
-          -e '$empty_text' 
+          -e '$empty_text'
         #end if
         -
         #echo ' '.join(['"%s"' % x for x in $extract.split()])
@@ -28,10 +29,8 @@
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
         <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" 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" help="Represent empty fields with this value, rather than leaving them blank" >
-        </param>
+        <param name="separator" type="text" value="" 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 name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" />
     </inputs>
     <outputs>
         <data format="tabular" name="output" />
@@ -78,13 +77,13 @@
         ID
         REF
         ALT
-        FILTER 
+        FILTER
     INFO fields:
         AF
         AC
         DP
         MQ
-        etc. (any info field available) 
+        etc. (any info field available)
     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.)
@@ -104,7 +103,7 @@
         "ANN[*].AA_POS" (alias POS_AA)
         "ANN[*].AA_LEN" (alias LEN_AA)
         "ANN[*].DISTANCE"
-        "ANN[*].ERRORS" (alias WARNING, INFOS) 
+        "ANN[*].ERRORS" (alias WARNING, INFOS)
     SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field):
         "EFF[*].EFFECT"
         "EFF[*].IMPACT"
@@ -116,17 +115,17 @@
         "EFF[*].BIOTYPE"
         "EFF[*].CODING"
         "EFF[*].TRID"
-        "EFF[*].RANK" 
+        "EFF[*].RANK"
     SnpEff 'LOF' fields:
         "LOF[*].GENE"
         "LOF[*].GENEID"
         "LOF[*].NUMTR"
-        "LOF[*].PERC" 
+        "LOF[*].PERC"
     SnpEff' NMD' fields:
         "NMD[*].GENE"
         "NMD[*].GENEID"
         "NMD[*].NUMTR"
-        "NMD[*].PERC" 
+        "NMD[*].PERC"
 
 
 Some examples:
@@ -135,7 +134,7 @@
 
     **CHROM POS ID AF**
 
-    The result will look something like: 
+    The result will look something like:
 
       ::
 
@@ -155,25 +154,25 @@
       - GEN[0].GL[1] : Second likelihood from first genotype
       - GEN[1].GL : The whole GL fiels (all entries without separating them)
       - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
-      - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated). 
+      - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
 
-    The result will look something like: 
+    The result will look something like:
 
       ::
 
         #CHROM  POS     ID              THETA   GEN[0].GL[1]    GEN[1].GL               GEN[3].GL[*]            GEN[*].GT
-        1       10583   rs58108140      0.0046  -0.47           -0.24,-0.44,-1.16       -0.48   -0.48   -0.48   0|0     0|0     0|0     0|1     0|0     0|1     0|0     0|0     0|1 
-        1       10611   rs189107123     0.0077  -0.48           -0.24,-0.44,-1.16       -0.48   -0.48   -0.48   0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|0     0|0 
-        1       13302   rs180734498     0.0048  -0.58           -2.45,-0.00,-5.00       -0.48   -0.48   -0.48   0|0     0|1     0|0     0|0     0|0     1|0     0|0     0|1     0|0 
+        1       10583   rs58108140      0.0046  -0.47           -0.24,-0.44,-1.16       -0.48   -0.48   -0.48   0|0     0|0     0|0     0|1     0|0     0|1     0|0     0|0     0|1
+        1       10611   rs189107123     0.0077  -0.48           -0.24,-0.44,-1.16       -0.48   -0.48   -0.48   0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|0     0|0
+        1       13302   rs180734498     0.0048  -0.58           -2.45,-0.00,-5.00       -0.48   -0.48   -0.48   0|0     0|1     0|0     0|0     0|0     1|0     0|0     0|1     0|0
 
   - *Extracting fields with multiple values:*
     (notice that there are multiple effect columns per line because there are mutiple effects per variant)
 
     **CHROM POS REF ALT ANN[*].EFFECT**
 
-    The result will look something like: 
+    The result will look something like:
 
-      :: 
+      ::
 
         #CHROM	POS	REF	ALT	ANN[*].EFFECT
         22	17071756	T	C	3_prime_UTR_variant	downstream_gene_variant
@@ -184,9 +183,9 @@
 
     **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
 
-    The result will look something like: 
+    The result will look something like:
 
-      :: 
+      ::
 
         #CHROM	POS	REF	ALT	ANN[*].EFFECT	ANN[*].HGVS_P
         22	17071756	T	C	3_prime_UTR_variant,downstream_gene_variant	.,.
@@ -198,9 +197,9 @@
 
     **CHROM POS REF ALT ANN[*].EFFECT**
 
-    The result will look something like: 
+    The result will look something like:
 
-      :: 
+      ::
 
         #CHROM	POS	REF	ALT	ANN[*].EFFECT
         22	17071756	T	C	3_prime_UTR_variant
--- a/snpSift_filter.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_filter.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.1">
     <description>Filter variants using arbitrary expressions</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -8,7 +8,8 @@
     <expand macro="version_command" />
 
     <command><![CDATA[
-        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse 
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse
         #if $filtering.mode == 'field':
             #if $filtering.replace.pass:
                 --pass
@@ -29,7 +30,7 @@
     <configfiles>
         <configfile name="exprFile">
 $expr#slurp
-        </configfile> 
+        </configfile>
     </configfiles>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -41,20 +42,19 @@
             <param name="mode" type="select" label="Filter mode">
                 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
                 <option value="field">Change the FILTER field, but retain all entries</option>
-            </param> 
+            </param>
             <when value="entries"/>
             <when value="field">
                 <conditional name="replace">
-                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 
+                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
                            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)." 
-                               help="Default ID is 'SnpSift'"/>
+                        <param name="filterId" type="text" value="" 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." />
-                <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)." />
+                <param name="addFilter" type="text" value="" label="Add a string to FILTER VCF field if 'expression' is true." />
+                <param name="rmFilter" type="text" value="" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
             </when>
         </conditional>
     </inputs>
@@ -133,20 +133,20 @@
 
     ::
 
-    (FILTER = 'PASS') | ( na FILTER )  
+    (FILTER = 'PASS') | ( na FILTER )
 
   - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
 
     ::
-  
+
     ( ANN[*].EFFECT has 'frameshift_variant' )
 
-    **Important** According to the specification, there can be more than one EFFECT separated by & (e.g. 'missense_variant&splice_region_variant', thus using has operator is better than using equality operator (=). For instance 'missense_variant&splice_region_variant' = 'missense_variant' is false, whereas 'missense_variant&splice_region_variant' has 'missense_variant' is true. 
+    **Important** According to the specification, there can be more than one EFFECT separated by & (e.g. 'missense_variant&splice_region_variant', thus using has operator is better than using equality operator (=). For instance 'missense_variant&splice_region_variant' = 'missense_variant' is false, whereas 'missense_variant&splice_region_variant' has 'missense_variant' is true.
 
   - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
 
     ::
-  
+
     ( EFF[*].EFFECT = 'FRAME_SHIFT' )
 
   - *I want to filter out samples with quality less than 30*:
@@ -160,23 +160,23 @@
     ::
 
     (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any homozygous variant present in more than 3 samples*:
 
     ::
 
     (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any heterozygous sample with coverage 25 or more*:
 
     ::
 
     ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
 
     ::
-  
+
     (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
 
 
--- a/snpSift_int.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_int.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1">
     <description>Filter variants using intervals</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
@@ -10,7 +10,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
 ]]>
     </command>
     <inputs>
--- a/snpSift_macros.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_macros.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.1">snpsift</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,8 +10,12 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
   <xml name="version_command">
-    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</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@">
@@ -20,16 +24,6 @@
 	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
-  <token name="@CITATION_SECTION@">------
-
-**Citation**
-
-For the underlying tool, please cite the following two publications:
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
-
-  </token>
   <xml name="citations">
       <citations>
         <citation type="doi">10.3389/fgene.2012.00035</citation>
--- a/snpSift_rmInfo.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_rmInfo.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.1">
     <description>remove INFO field annotations</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -7,7 +7,10 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" rmInfo "$input" ' '.join($info_fields.split(',')) > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" rmInfo "$input"
+        #echo ' '.join($info_fields.split(','))
+        > "$output"
 ]]>
     </command>
     <inputs>
@@ -22,7 +25,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/>
+            <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
             <param name="info_fields" value="EFF"/>
             <output name="output">
                 <assert_contents>
@@ -31,15 +34,6 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/>
-            <param name="info_fields" value="EFF"/>
-            <output name="output">
-                <assert_contents>
-                    <not_has_text text="DP=29;EFF=EXON" />
-                </assert_contents>
-            </output>
-        </test>
     </tests>
     <help><![CDATA[
 This command removes INFO fields from a VCF file (i.e. removes annotations)
--- a/snpSift_vartype.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_vartype.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
+<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.1">
     <description>Annotate with variant type</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -7,7 +7,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
 ]]>
     </command>
     <inputs>
@@ -33,10 +34,7 @@
 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-@CITATION_SECTION@
-
+.. _MIT license: https://opensource.org/licenses/MIT
 ]]>
     </help>
     <expand macro="citations" />
--- a/snpSift_vcfCheck.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_vcfCheck.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,5 +1,5 @@
-<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
-    <description>basic checks for Vcf specification compliance</description>
+<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
+    <description>basic checks for VCF specification compliance</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
@@ -7,7 +7,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -18,23 +19,19 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
-            <output name="output">
-                <assert_contents>
-                    <has_text text="Errors" />
-		</assert_contents>
-            </output>
+            <param name="input" ftype="vcf" value="test_bad.vcf"/>
+            <assert_stderr>
+                <has_text text="Errors" />
+            </assert_stderr>
         </test>
     </tests>
     <help><![CDATA[
-
 Perform some basic check ups on VCF files to spot common problems.
 
 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 
 
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
-
 ]]>
     </help>
     <expand macro="citations" />
--- a/tool_dependencies.xml	Tue Jun 07 10:04:09 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="snpEff" version="4.1">
-        <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>