Mercurial > repos > iuc > snpsift

diff snpSift_extractFields.xml @ 3:20c7d583fec1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
line wrap: on
line diff
--- a/snpSift_extractFields.xml	Mon Dec 05 12:11:18 2016 -0500
+++ b/snpSift_extractFields.xml	Mon Jun 12 10:25:32 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.1">
+<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">
     <options sanitize="False" />
     <description>from a VCF file into a tabular file</description>
     <macros>
@@ -8,32 +8,31 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPSIFT_JAR_PATH@ &&
-        cat "$input"
-        #if $one_effect_per_line:
-          | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
-        #end if
-        | java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" extractFields
-        #if $separator:
-          -s '$separator'
-        #end if
-        #if $empty_text:
-          -e '$empty_text'
-        #end if
-        -
-        #echo ' '.join(['"%s"' % x for x in $extract.split()])
-        > "$output"
-]]>
-    </command>
+@CONDA_SNPSIFT_JAR_PATH@ &&
+cat '$input'
+#if $one_effect_per_line:
+    | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
+#end if
+| SnpSift -Xmx6G extractFields
+#if $separator:
+    -s '$separator'
+#end if
+#if $empty_text:
+    -e '$empty_text'
+#end if
+-
+#echo ' '.join(['"%s"' % x for x in $extract.split()])
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <param name="input" type="data" format="vcf" 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="" 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" />
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test>
@@ -57,19 +56,15 @@
                 </assert_contents>
             </output>
         </test>
-
     </tests>
     <help><![CDATA[
-
 **SnpSift Extract Fields**
 
 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc.
 
 http://snpeff.sourceforge.net/SnpSift.html#Extract
 
-You can also use sub-fields and genotype fields / sub-fields such as:
-
-  ::
+You can also use sub-fields and genotype fields / sub-fields such as::
 
     Standard VCF fields:
         CHROM
@@ -127,93 +122,77 @@
         "NMD[*].NUMTR"
         "NMD[*].PERC"
 
-
 Some examples:
 
-  - *Extracting chromosome, position, ID and allele frequency from a VCF file:*
-
-    **CHROM POS ID AF**
+- *Extracting chromosome, position, ID and allele frequency from a VCF file*:
 
-    The result will look something like:
+  **CHROM POS ID AF**
 
-      ::
+  The result will look something like::
 
-        #CHROM        POS        ID            AF
-        1             69134                    0.086
-        1             69496      rs150690004   0.001
-
+      #CHROM        POS        ID            AF
+      1             69134                    0.086
+      1             69496      rs150690004   0.001
 
-  - *Extracting genotype fields:*
+- *Extracting genotype fields*:
 
-    **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
+  **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
 
-    This means to extract:
+  This means to extract:
 
-      - CHROM POS ID: regular fields (as in the previous example)
-      - THETA : This one is from INFO
-      - 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).
-
-    The result will look something like:
+  - CHROM POS ID: regular fields (as in the previous example)
+  - THETA : This one is from INFO
+  - 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).
 
-      ::
+  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
+      #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
 
-  - *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**
+- *Extracting fields with multiple values*:
+  (notice that there are multiple effect columns per line because there are mutiple effects per variant)
 
-    The result will look something like:
+  **CHROM POS REF ALT ANN[*].EFFECT**
 
-      ::
+  The result will look something like::
 
-        #CHROM	POS	REF	ALT	ANN[*].EFFECT
-        22	17071756	T	C	3_prime_UTR_variant	downstream_gene_variant
-        22	17072035	C	T	missense_variant	downstream_gene_variant
-        22	17072258	C	A	missense_variant	downstream_gene_variant
+      #CHROM	POS	REF	ALT	ANN[*].EFFECT
+      22	17071756	T	C	3_prime_UTR_variant	downstream_gene_variant
+      22	17072035	C	T	missense_variant	downstream_gene_variant
+      22	17072258	C	A	missense_variant	downstream_gene_variant
 
-  - *Extracting fields with multiple values using a comma as a multipe field separator:*
-
-    **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
+- *Extracting fields with multiple values using a comma as a multipe field separator:*
 
-    The result will look something like:
+  **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
 
-      ::
+  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	.,.
-        22	17072035	C	T	missense_variant,downstream_gene_variant	p.Gly469Glu,.
-        22	17072258	C	A	missense_variant,downstream_gene_variant	p.Gly395Cys,.
+      #CHROM	POS	REF	ALT	ANN[*].EFFECT	ANN[*].HGVS_P
+      22	17071756	T	C	3_prime_UTR_variant,downstream_gene_variant	.,.
+      22	17072035	C	T	missense_variant,downstream_gene_variant	p.Gly469Glu,.
+      22	17072258	C	A	missense_variant,downstream_gene_variant	p.Gly395Cys,.
 
+- *Extracting fields with multiple values, one effect per line:*
 
-  - *Extracting fields with multiple values, one effect per line:*
-
-    **CHROM POS REF ALT ANN[*].EFFECT**
+  **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
-        22	17071756	T	C	downstream_gene_variant
-        22	17072035	C	T	missense_variant
-        22	17072035	C	T	downstream_gene_variant
-        22	17072258	C	A	missense_variant
-        22	17072258	C	A	downstream_gene_variant
-
+      #CHROM	POS	REF	ALT	ANN[*].EFFECT
+      22	17071756	T	C	3_prime_UTR_variant
+      22	17071756	T	C	downstream_gene_variant
+      22	17072035	C	T	missense_variant
+      22	17072035	C	T	downstream_gene_variant
+      22	17072258	C	A	missense_variant
+      22	17072258	C	A	downstream_gene_variant
 
 @EXTERNAL_DOCUMENTATION@
-	http://snpeff.sourceforge.net/SnpSift.html#Extract
-
-]]>
-    </help>
+- http://snpeff.sourceforge.net/SnpSift.html#Extract
+    ]]></help>
     <expand macro="citations" />
 </tool>