changeset 1:01bd7d27089d draft

Deleted selected files

--- a/vcfs2fasta/vcfs2fasta.xml	Wed Dec 16 07:21:29 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-<tool id="vcfs2fasta" name="VCFs to fasta" version="1.0">
-  <description>Takes a set of VCF files and outputs a multi fasta file with only the variant positions.</description>
-  <requirements>
-    <requirement type="package" version="2.7.10">python</requirement>
-    <requirement type="package" version="0.6.7">pyvcf</requirement>
-    <requirement type="package" version="3.11">pyyaml</requirement>
-    <requirement type="package" version="2.0.2">bintrees</requirement>
-	<requirement type="package" version="1.66">biopython</requirement>
-	<requirement type="package" version="1.4">matplotlib</requirement>
-  </requirements>
-  <stdio>
-	<!-- Assume anything other than zero is an error -->
-    <exit_code range="1:" />
-    <exit_code range=":-1" />
-  </stdio>
-  <command interpreter="bash">
-    vcfs2fasta.sh
-	$output
-	#if str($mix_cond.mix) == "yes":
-        $mix_cond.mix_value
-    #else
-        NOTTHERE
-    #end if
-	#if str($cols_cond.cols) == "yes":
-        $cols_cond.column_ns
-    #else
-        NOTTHERE
-    #end if
-	#if str($sample_cond.sample) == "yes":
-        $sample_cond.sample_ns
-    #else
-        NOTTHERE
-    #end if
-	#if str($reference_cond.reference) == "yes":
-		$reference_cond.ref_fa
-	#else
-        NOTTHERE
-    #end if
-	#if str($include_cond.include) == "yes":
-		$include_cond.in_bed
-	#else
-        NOTTHERE
-    #end if
-	#if str($exclude_cond.exclude) == "yes":
-		$exclude_cond.ex_bed
-	#else
-        NOTTHERE
-    #end if
-	#for $i, $input_vcf in enumerate( $input_vcfs ):
-        "${input_vcf}"
-    #end for
-  </command>
-
-  <inputs>
-	<param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
-	<conditional name="mix_cond">
-        <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="mix_value" type="float" value="0.5" label="Mixture value" />
-        </when>
-    </conditional>
-	<conditional name="cols_cond">
-        <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns above specified threshold.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="column_ns" type="float" value="0.5" label="Column Ns value" />
-        </when>
-    </conditional>
-	<conditional name="sample_cond">
-        <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns above specified threshold.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
-        </when>
-    </conditional>
-	<conditional name="reference_cond">
-        <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
-        </when>
-    </conditional>
-	<conditional name="include_cond">
-        <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
-        </when>
-    </conditional>
-	<conditional name="exclude_cond">
-        <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file.">
-          <option value="yes">Specify</option>
-          <option value="no" selected="true">Do not specify</option>
-        </param>
-        <when value="yes">
-			<param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
-        </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" />
-  </outputs>
-  <test>
-	<param name="input_vcfs" value="1_short.vcf" ftype="vcf" />
-	<param name="input_vcfs" value="2_short.vcf" ftype="vcf" />
-	<output name="output" file="testresult.fa" ftype="fasta" />
-  </test>
-  <help>
-
-  </help>
-</tool>