changeset 2:ea72be8a5804 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty

--- a/bcftools_consensus.xml	Sun Jun 26 15:33:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
-    <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
-    <macros>
-        <token name="@EXECUTABLE@">consensus</token>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
-    <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
-@PREPARE_INPUT_FILE@
-#set $section = $sec_default
-@PREPARE_FASTA_REF@
-
-bcftools @EXECUTABLE@
-
-## Default section
-#set $section = $sec_default
-@FASTA_REF@
-
-${section.iupac_codes}
-
-#if $section.mask:
-  --mask "${section.mask}"
-#end if
-
-#if $section.select_haplotype:
-  --haplotype "${section.select_haplotype}"
-#end if
-@SAMPLE@
-
-#if $chain:
-  --chain "$chain_file"
-#end if
-
-## Primary Input/Outputs
---output "$output_file"
-@INPUT_FILE@
-]]>
-    </command>
-    <inputs>
-        <expand macro="macro_input" />
-        <section name="sec_default" expanded="true" title="Default Options">
-            <expand macro="macro_fasta_ref" />
-            <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
-
-            <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" 
-                   help="Output variants in the form of IUPAC ambiguity codes" />
-            <expand macro="macro_sample" />
-            <param name="select_haplotype" type="select" optional="true">
-                <option value="1">1</option>
-                <option value="2">2</option>
-            </param>
-        </section>
-        <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
-    </inputs>
-    <outputs>
-        <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
-        <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
-            <filter>chain</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="reference_fasta" ftype="fasta" value="consensus.fa" />
-            <param name="input_file" ftype="vcf" value="consensus.vcf" />
-            <param name="mask" ftype="tabular" value="consensus.tab" />
-            <param name="chain" value="True" />
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
-                </assert_contents>
-            </output>
-            <output name="chain_file">
-                <assert_contents>
-                    <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
-                </assert_contents>
-            </output>
-            <output name="chain_file" file="consensus.1.chain" />
-    </tests>
-    <help><![CDATA[
-=====================================
- bcftools @EXECUTABLE@ plugin
-=====================================
-
-
-Create consensus sequence by applying VCF variants to a reference fasta file.
-
-@BCFTOOLS_MANPAGE@#@EXECUTABLE@
-
-@BCFTOOLS_WIKI@
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>