Mercurial > repos > gandres > vcftools_filter_stats_diversity
changeset 8:2b6bb9d5e4e9 draft
planemo upload
| author | gandres |
|---|---|
| date | Tue, 12 Apr 2016 05:43:01 -0400 |
| parents | ca045c1d5fa5 |
| children | ce984119f669 |
| files | VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh VCFToolsStats/vcfToolsStats.sh VCFToolsStats/vcfToolsStats.xml test-data/stats-result.annotation |
| diffstat | 4 files changed, 16 insertions(+), 39 deletions(-) [+] |
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--- a/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh Thu Mar 31 10:41:59 2016 -0400 +++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh Tue Apr 12 05:43:01 2016 -0400 @@ -23,7 +23,16 @@ cp $filein ${filein}.vcf if [ "$group" != "none" ] -then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window --group $group +then + if [ $(sort -k2,2 -t ';' -u $group | cut -f2 -d ';' |wc -l) -ge 3 ] + then + echo 'ERROR: it only works with 2 groups. There is too many groups in your file.' >&2 + exit 1 + else + perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window --group $group + fi + + else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window fi
--- a/VCFToolsStats/vcfToolsStats.sh Thu Mar 31 10:41:59 2016 -0400 +++ b/VCFToolsStats/vcfToolsStats.sh Tue Apr 12 05:43:01 2016 -0400 @@ -4,17 +4,15 @@ filein=$1 fileout_label=$(date "+%Y%m%d%H%M%S") -fileout_annot=$2 -fileout_het=$3 -fileout_imiss=$4 -fileout_sum=$5 -filelog=$6 +fileout_het=$2 +fileout_imiss=$3 +fileout_sum=$4 +filelog=$5 perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label -cp $fileout_label.annotation $fileout_annot ; rm $fileout_label.annotation cp $fileout_label.het $fileout_het ; rm $fileout_label.het cp $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss cp $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary
--- a/VCFToolsStats/vcfToolsStats.xml Thu Mar 31 10:41:59 2016 -0400 +++ b/VCFToolsStats/vcfToolsStats.xml Tue Apr 12 05:43:01 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.1.0"> +<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.2.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> @@ -17,7 +17,7 @@ <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> - vcfToolsStats.sh $filein $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog + vcfToolsStats.sh $filein $fileout_het $fileout_imiss $fileout_sum $filelog </command> <!-- [REQUIRED] Input files and tool parameters --> @@ -28,7 +28,6 @@ <!-- [REQUIRED] Output files --> <outputs> - <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" /> <data name="fileout_het" format="txt" label="${fileout_label}.het" /> <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> @@ -40,7 +39,6 @@ <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="filein" value="sample.vcf" /> - <output name="fileout_annot" file="stats-result.annotation" /> <output name="fileout_het" file="stats-result.het" /> <output name="fileout_imiss" file="stats-result.imiss" /> <output name="fileout_sum" file="stats-result.TsTv.summary" /> @@ -120,9 +118,6 @@ Output files ------------ -.annotation file - Statistics on annotation/location along genome - .het file Statistics on heterozygosity of the individuals @@ -163,22 +158,6 @@ Output files ============ - -.annotation file ----------------- - -:: - - Genic 4489 - Intergenic 466 - ======== - Intron 960 - Exon 3248 - UTR 281 - ======== - Non-syn 226 - Synonym 3022 - .het file ---------