Mercurial > repos > devteam > vcfgeno2haplo

changeset 2:5bd9783e982a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:06:33 -0400
parents 401f29f278f0
children b890055e07bd
files macros.xml tool_dependencies.xml vcfgeno2haplo.xml
diffstat 3 files changed, 77 insertions(+), 82 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Nov 11 13:00:04 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:06:33 2016 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,6 +10,7 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
+   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
    	<xml name="citations">
    	     <citations>
              <citation type="bibtex">
--- a/tool_dependencies.xml	Wed Nov 11 13:00:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcflib" version="8a5602bf07">
-        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- a/vcfgeno2haplo.xml	Wed Nov 11 13:00:04 2015 -0500
+++ b/vcfgeno2haplo.xml	Thu Sep 15 16:06:33 2016 -0400
@@ -1,75 +1,75 @@
-<tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.3">
-  <description>Convert genotype-based phased alleles into haplotype alleles</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <command>
-    #set $reference_fasta_filename = "localref.fa"
-    #if str( $reference_source.reference_source_selector ) == "history":
-       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
-    #else:
-       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-    #end if    
-  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
-  <inputs>
-    <conditional name="reference_source">
-       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
-         <option value="cached">Locally cached</option>
-         <option value="history">History</option>
-       </param>
-       <when value="cached">
-         <param name="ref_file" type="select" label="Select reference genome">
-           <options from_data_table="fasta_indexes">
-             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
-           </options>
-	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-         </param>
-	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
-	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
-		<validator type="unspecified_build" />
-		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-	   -->
-	 </param>
-       </when>
-       <when value="history"> <!-- FIX ME!!!! -->
-         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
-       </when>
-     </conditional>
-     <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
-     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
-<!--       <option value=" ">Output entire haplotype</option>
-       <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
-     </param> -->
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="reference_source_selector" value="history" />
-      <param name="output_option" value="true" />
-      <param name="window_size" value="5000" />
-      <param name="input_vcf" value="vcflib-phix.vcf"/>
-      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
-      <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
-    </test>
-    </tests>
-  <help>
-
-Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
-
-The options are::
-
-    -w, --window-size N     Merge variants at most this many bp apart (default 30)
-    -o, --only-variants     Don't output the entire haplotype, just concatenate
-                            REF/ALT strings (delimited by ":")
-
-----
-
-Vcfgeno2haplo @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="@WRAPPER_VERSION@.0">
+  <description>Convert genotype-based phased alleles into haplotype alleles</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if    
+  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+    <conditional name="reference_source">
+       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+         <option value="cached">Locally cached</option>
+         <option value="history">History</option>
+       </param>
+       <when value="cached">
+         <param name="ref_file" type="select" label="Select reference genome">
+           <options from_data_table="fasta_indexes">
+             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
+           </options>
+	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+         </param>
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
+	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
+		<validator type="unspecified_build" />
+		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+	   -->
+	 </param>
+       </when>
+       <when value="history"> <!-- FIX ME!!!! -->
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
+       </when>
+     </conditional>
+     <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
+     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
+<!--       <option value=" ">Output entire haplotype</option>
+       <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
+     </param> -->
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="output_option" value="true" />
+      <param name="window_size" value="5000" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
+
+The options are::
+
+    -w, --window-size N     Merge variants at most this many bp apart (default 30)
+    -o, --only-variants     Don't output the entire haplotype, just concatenate
+                            REF/ALT strings (delimited by ":")
+
+----
+
+Vcfgeno2haplo @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>