Mercurial > repos > urgi-team > vcfgandalftools
diff VCFGandalfTools/VCFCarto_wrapper.xml @ 2:6bebeb76fa8d draft
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| author | urgi-team |
|---|---|
| date | Tue, 05 Apr 2016 08:33:41 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFGandalfTools/VCFCarto_wrapper.xml Tue Apr 05 08:33:41 2016 -0400 @@ -0,0 +1,315 @@ +<tool id="VCFCarto" name="VCFCarto" version="0.01"> + <description>VCFcarto can convert a tabulated marker file into a file with only the markers from 2 parents </description> + <requirements> + <requirement type="package" version="1.0">VCF_Gandalf_Tools</requirement> + </requirements> + <version_command> + VCFCarto.py --version + </version_command> + <command interpreter="python"> + VCFCarto_wrapper.py -f $inputTabular -o $outputVCFCarto -A $parentA -H $parentH + #if str($outputType) == "carto" + -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path" + #end if + #if str($outputType) == "MergedCarto" + -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path" -m --mergeFile $output_bed + #end if + </command> + <inputs> + <param name="inputTabular" type="data" format="tabular" label="indicate your tabulated marker file"/> + <param name="parentA" size="20" type="text" value="V1" label="indicate parent 1 name (A)"/> + <param name="parentH" size="20" type="text" value="V2" label="indicate parent 2 name (H)"/> + <param name="outputType" type="select" display="radio" label="select type of output" multiple="False"> + <option value="raw" >7 caracter code</option> + <option value="carto" >A - H code</option> + <option value="MergedCarto" >A - H code and merge</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="outputVCFCarto" label="${tool.name} on ${on_string} (tabular)"/> + <data format="html" name="output_html" label="${tool.name} graphs on ${on_string} (html)"> + <filter>not outputType == "raw"</filter> + </data> + <data format="bed" name="output_bed" label="${tool.name} markers on ${on_string} (bed)"> + <filter>outputType == "MergedCarto"</filter> + </data> + </outputs> + <tests> + <test> + <param name="inputTabular" value="VCFCarto_input.tab"/> + <param name="parentA" value="REF1"/> + <param name="parentH" value="REF2"/> + <param name="outputType" value="raw"/> + <output name="outputVCFCarto" file="VCFCarto_output.tab" ftype="tabular"/> + </test> + <test> + <param name="inputTabular" value="VCFCarto_input.tab"/> + <param name="parentA" value="REF1"/> + <param name="parentH" value="REF2"/> + <param name="outputType" value="MergedCarto"/> + <output name="outputVCFCarto" file="VCFCarto_output_merged.tab" ftype="tabular"/> + <output name="output_bed" file="VCFCarto_output_merged.bed" ftype="bed"/> + </test> + </tests> + <help><![CDATA[ + +**VCFcarto converts a tabulated marker file into a file with only the markers from 2 parents** + +.. class:: infomark + +expected input format is the output from VCFStorage. + +----- + +**what it does :** + +VCFcarto converts a tabulated marker file into a file with only the markers from 2 parents, refA and refH. + +2 formats are possible, either the input format is conserved, or the format is changed into a 3 letter format + +----- + +**input format :** + +.. class:: infomark + +expected input format is the output from VCFStorage. + +the expected format is a tab delimited format file where all genomic positions are in rows, and all strains are in columns + +For each position and each genome, a code is attributed : + +- for the reference : :: + + A,T,G,C for the corresponding nucleotidic acid + +- for the genomes : :: + + U if the position was not refered in the VCF file + R if the base is similar to the reference + F if the base has been filtered out + A,T,G,C if the genome has a validated SNP at the position + +----- + +**output format :** + +for the main output, 2 formats are possible : + +- The first format is similar to the input format (same columns and code) but will only be conserved lines where the 2 parents have different alleles. + +- The second format (A - H format) will have a much simpler code :: + + "A" when the strain allele is the same as parent A + "H" when the strain allele is the same as parent H + "-" in any other case (base filtered out, different base, base unmapped etc...) + +the second format may be used as an input for a cartographic tool. + +If you decide to have the A - H format, you can also merge consecutive markers that carries the same information (every strains are similars between the two markers). If you decide to do so, new markers will be generated and a bed file will do the link between the input and the output markers. + +Finally, graphical output will be displayed to visualise the result. + +----- + +**example :** + +input : :: + + CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 + Chr1 1 A R R R R U R R R R R R R R R + Chr1 2 T R R R R R U R R R R R R R R + Chr1 3 G R R R R R R R R R R R R R R + Chr1 4 G R R R R R R R R R R R R F R + Chr1 5 G R R R R R R U F R R R R R R + Chr1 6 C R R R R R R R R R R R R R U + Chr1 7 A G C C C F C C C C C G C G G + Chr1 8 G R R R R R R R R R R R R R R + Chr1 9 C R T T R T T T U R T R T T T + Chr1 10 T R R R R R R R R R R R R R U + Chr1 11 T R R R R R R R R R R R F R R + Chr1 12 A R R R R U R R R R F R R R R + Chr1 13 A R R G G R F R F G R G R R F + Chr1 14 A R R R R R R R R F R R R R R + Chr1 15 G R R R U R F R R R R R R U U + Chr1 16 G A R R A R R U F R R A A R A + Chr1 17 A R G G R U R R G G R G U R G + Chr1 18 C R R R R R U R R R R R R R R + Chr1 19 G C U R C R C U R R C C C R C + Chr1 20 G A U R A R A U R R A A A R A + Chr1 21 G T U R T R T U R R T T T R T + Chr1 22 A T U R T R T U R R T T T R T + Chr1 23 C T T R T R R R T R U T R T T + Chr1 24 T R R R R R U R R R R R R R F + Chr1 25 G R F R R R R R U R F R R R R + Chr1 26 T R R C C C C C R R C R C R U + Chr1 27 C R R G G G G R G R G R G R R + Chr1 28 C G T T T G G T T F T G T T G + Chr1 29 G T R R R R T R T R T T R T R + Chr1 30 T R R R R R R R R R R R R R R + Chr1 31 A R R R R F R R R R F R R R R + Chr1 32 A G G R G G G R R G G G G G R + Chr1 33 G R R R R R R R R R R R R R R + Chr1 34 C R R R R R R R R R R R R R R + Chr1 35 C R R R R R F R R R R R R R U + Chr2 1 T R R R F R R R R R R R R R R + Chr2 2 A C R R C C U R R R R C C C U + Chr2 3 C R R R R R R U R R R R R R R + Chr2 4 C R R R R R R R U R R R R F R + Chr2 5 T R R R R R R R R R R R R R R + Chr2 6 C R R R R R R R R R R R R R R + Chr2 7 A T F R U R T T T R T T F T T + Chr2 8 T R R R R R R R R R R R R R R + Chr2 9 C R R R R R R R R R R R R R R + Chr2 10 G R T T T T R T R R R R R U R + Chr2 11 C R A A A A R A R R R R R U R + Chr2 12 A R T T T T R T R R R R R U R + Chr2 13 T R C C C C R C R R R R R U R + Chr2 14 C T A A T A T A T A T T A A A + Chr2 15 T R R R F R R R R R R R R R R + Chr2 16 A R R R R R R R U R R R R R R + Chr2 17 A R U R R R R R R R R R R R F + Chr2 18 G R R R R R R R R R R R R R R + Chr2 19 A R R R R R R F R R R R R R R + Chr2 20 C R R R R R R R F R R R R R R + Chr2 21 G A R R A A A R R R A A R R R + Chr2 22 A R R R R R R F R R R R R R R + Chr2 23 A R R T T R R T T T T T R R R + Chr2 24 T R R R R R R U R R R R R R F + Chr2 25 T R A A R R A R A R R A R R A + Chr2 26 G R R R R R R R R R R R R R R + Chr2 27 A R R R R R R R R R R R R U R + Chr2 28 C R U R R F F R R F R F U R R + Chr2 29 G R R R R R R F R R R R R R R + Chr2 30 T A A G A G G A A G F G G G U + Chr2 31 A R R R R R R R R U U R R R R + Chr2 32 G R R R R R R U U R R R R R R + Chr2 33 G R U R R R R U R R R R R R R + Chr2 34 A R R R U R R R R R R R R R R + Chr2 35 G R R R R R R R R R R R R R R + Chr2 36 T R R R R R R U R R R R R R R + Chr3 1 T U R R R R R U R R R R R R R + Chr3 2 T R R U R R R U R R R R R R R + Chr3 3 T F R R R R R U R R R R R R R + Chr3 4 T R R F R R R U R R R R R R R + + +output : + +- without A - H code : :: + + CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 + Chr1 7 A G C C C F C C C C C G C G G + Chr1 9 C R T T R T T T U R T R T T T + Chr1 13 A R R G G R F R F G R G R R F + Chr1 16 G A R R A R R U F R R A A R A + Chr1 17 A R G G R U R R G G R G U R G + Chr1 19 G C U R C R C U R R C C C R C + Chr1 20 G A U R A R A U R R A A A R A + Chr1 21 G T U R T R T U R R T T T R T + Chr1 22 A T U R T R T U R R T T T R T + Chr1 23 C T T R T R R R T R U T R T T + Chr1 26 T R R C C C C C R R C R C R U + Chr1 27 C R R G G G G R G R G R G R R + Chr1 28 C G T T T G G T T F T G T T G + Chr1 29 G T R R R R T R T R T T R T R + Chr1 32 A G G R G G G R R G G G G G R + Chr2 2 A C R R C C U R R R R C C C U + Chr2 7 A T F R U R T T T R T T F T T + Chr2 10 G R T T T T R T R R R R R U R + Chr2 11 C R A A A A R A R R R R R U R + Chr2 12 A R T T T T R T R R R R R U R + Chr2 13 T R C C C C R C R R R R R U R + Chr2 14 C T A A T A T A T A T T A A A + Chr2 21 G A R R A A A R R R A A R R R + Chr2 23 A R R T T R R T T T T T R R R + Chr2 25 T R A A R R A R A R R A R R A + Chr2 30 T A A G A G G A A G F G G G U + +- with A - H code but no markers : :: + + CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 + Chr1 7 - A H H H - H H H H H A H A A + Chr1 9 - A H H A H H H - A H A H H H + Chr1 13 - A A H H A - A - H A H A A - + Chr1 16 - A H H A H H - - H H A A H A + Chr1 17 - A H H A - A A H H A H - A H + Chr1 19 - A - H A H A - H H A A A H A + Chr1 20 - A - H A H A - H H A A A H A + Chr1 21 - A - H A H A - H H A A A H A + Chr1 22 - A - H A H A - H H A A A H A + Chr1 23 - A A H A H H H A H - A H A A + Chr1 26 - A A H H H H H A A H A H A - + Chr1 27 - A A H H H H A H A H A H A A + Chr1 28 - A H H H A A H H - H A H H A + Chr1 29 - A H H H H A H A H A A H A H + Chr1 32 - A A H A A A H H A A A A A H + Chr2 2 - A H H A A - H H H H A A A - + Chr2 7 - A - H - H A A A H A A - A A + Chr2 10 - A H H H H A H A A A A A - A + Chr2 11 - A H H H H A H A A A A A - A + Chr2 12 - A H H H H A H A A A A A - A + Chr2 13 - A H H H H A H A A A A A - A + Chr2 14 - A H H A H A H A H A A H H H + Chr2 21 - A H H A A A H H H A A H H H + Chr2 23 - A A H H A A H H H H H A A A + Chr2 25 - A H H A A H A H A A H A A H + Chr2 30 - A A H A H H A A H - H H H - + +- with A - H code and merge : + + - tab file : :: + + CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 + Chr1 *M_00001 - A H H H - H H H H H A H A A + Chr1 *M_00002 - A H H A H H H - A H A H H H + Chr1 *M_00003 - A A H H A - A - H A H A A - + Chr1 *M_00004 - A H H A H H - - H H A A H A + Chr1 *M_00005 - A H H A - A A H H A H - A H + Chr1 *M_00006 - A - H A H A - H H A A A H A + Chr1 *M_00007 - A A H A H H H A H - A H A A + Chr1 *M_00008 - A A H H H H H A A H A H A - + Chr1 *M_00009 - A A H H H H A H A H A H A A + Chr1 *M_00010 - A H H H A A H H - H A H H A + Chr1 *M_00011 - A H H H H A H A H A A H A H + Chr1 *M_00012 - A A H A A A H H A A A A A H + Chr2 *M_00013 - A H H A A - H H H H A A A - + Chr2 *M_00014 - A - H - H A A A H A A - A A + Chr2 *M_00015 - A H H H H A H A A A A A - A + Chr2 *M_00016 - A H H A H A H A H A A H H H + Chr2 *M_00017 - A H H A A A H H H A A H H H + Chr2 *M_00018 - A A H H A A H H H H H A A A + Chr2 *M_00019 - A H H A A H A H A A H A A H + Chr2 *M_00020 - A A H A H H A A H - H H H - + + - bed file : :: + + Chr1 7 7 *M_00001 + Chr1 9 9 *M_00002 + Chr1 13 13 *M_00003 + Chr1 16 16 *M_00004 + Chr1 17 17 *M_00005 + Chr1 19 22 *M_00006 + Chr1 23 23 *M_00007 + Chr1 26 26 *M_00008 + Chr1 27 27 *M_00009 + Chr1 28 28 *M_00010 + Chr1 29 29 *M_00011 + Chr1 32 32 *M_00012 + Chr2 2 2 *M_00013 + Chr2 7 7 *M_00014 + Chr2 10 13 *M_00015 + Chr2 14 14 *M_00016 + Chr2 21 21 *M_00017 + Chr2 23 23 *M_00018 + Chr2 25 25 *M_00019 + Chr2 30 30 *M_00020 + + +----- + +**reference :** + +]]> + </help> +</tool>