annotate filterVCFonAnnotations.xml @ 2:15319113c0a5 draft

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<tool id="sniplay_filterVCFonAnnotations" name="Filter VCF on Annotations" version="1.0.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> </description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
    </requirements>
    
    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
    <version_command>
<!--
        tool_binary -v
-->
    </version_command>
    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="perl">
	FilterVCFonAnnotations.pl --input $filein --out $fileout 
	#if str( $genelist ) != "None":
	--genelist $genelist
	#end if
	#if str( $feature ) != "":
	--feature $feature
	#end if
	#if str( $syn ) != "":
	--syn $syn
	#end if
    </command>
     
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
	<param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
	<param name="genelist" type="data" format="txt" optional="true" label="Genelist" default="" help="File listing the genes to be filtered, one line per individu/gene"/>
	<param name="feature" type="select" label="Genomic feature" optional="true" help="Filter within genomic feature">
	    <option value="" selected="true">All</option>
	    <option value="Exon">Exon</option>
            <option value="INTRON">Intron</option>
            <option value="UTR_5_PRIME">UTR5prime</option>
            <option value="UTR_3_PRIME">UTR3prime</option>
            <option value="DOWNSTREAM">Downstream</option>
            <option value="UPSTREAM">Upstream</option>
	    <option value="INTERGENIC">Intergenic</option>
        </param>
        <param name="syn" type="select" label="Synonymous type" optional="true" help="Keep only synonymous, non-synonymous SNP">
            <option value="" selected="true">All</option>
            <option value="s">Synonymous</option>
            <option value="n">Non-synonymous</option>
        </param>
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout" type="data" format="vcf" label="${fileout_label}.vcf" />
    </outputs>
    
    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
        <test>
         <param name="filein" value="sample.vcf" />
         <param name="genelist" value="accession.txt" />
         <param name="feature" value="INTRON" />
         <output name="fileout" file="result.vcf" />
        </test>
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>

.. class:: infomark

**Authors** 

---------------------------------------------------

.. class:: infomark

**Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.

---------------------------------------------------

======================
Filter And Convert VCF
======================

-----------
Description
-----------

  Filter VCF file and convert in Fasta, Hapmap and PED

-----------------
Workflow position
-----------------

**Upstream tools**

=========== ========================== =======
Name            output file(s)         format 
=========== ========================== =======
=========== ========================== =======


**Downstream tools**

=========== ========================== =======
Name            output file(s)         format
=========== ========================== =======
=========== ========================== =======


----------
Input file
----------

VCF file
	VCF file with all SNPs

Genelist
	File listing the genes or individuals to be filtered. Gene_id or accesion number can be put in a file, one line per individual
	

----------
Parameters
----------

Output file name
	Prefix for the output VCF file

Genomic feature
        Filter on genomic feature : Exon,INTRON,UTR_3_PRIME,UTR_5_PRIME,DOWNSTREAM,UPSTREAM or INTERGENIC

Synonymous type
	Keep only synonymous, non-synonymous.


------------
Output files
------------

VCF file
	VCF file filtered 

---------------------------------------------------

---------------
Working example
---------------

Input files
===========

VCF file
---------

::

	#fileformat=VCFv4.1
	#FILTER=&lt;ID=LowQual,Description="Low quality">
	#FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
	[...]
	CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CATB1
	chr1	2209	.	G	T	213.84	.	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)	GT:AD:DP:GQ:PL	1/1:0,7:7:18:242,18,0

Genelist
---------

::

	Cc01g00020
	Cc01g00010

Parameters
==========

Output name -> filtered_genelist_intron

Genomic feature -> Intron

Output files
============

filtered_genelist_intron.vcf
----------------------------

::

        #fileformat=VCFv4.1
        #FILTER=&lt;ID=LowQual,Description="Low quality"&gt;
        #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
        [...]
        CHROM   POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CATB1
	chr1	5059	.	C	G	146.84	.	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)	GT:AD:DP:GQ:PL	1/1:0,8:8:18:175,18,0


    </help>
    
</tool>