Mercurial > repos > rico > test_single_file
changeset 6:e521b7111644
Uploaded
author | rico |
---|---|
date | Thu, 05 Apr 2012 15:13:44 -0400 |
parents | feeeee14729e |
children | 18dad59e1529 |
files | extract_flanking_dna.xml |
diffstat | 1 files changed, 93 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_flanking_dna.xml Thu Apr 05 15:13:44 2012 -0400 @@ -0,0 +1,93 @@ +<tool id="gd_extract_flanking_dna" name="Extract" version="1.0.0"> + <description>DNA flanking chosen SNPs</description> + + <command interpreter="python"> + extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc" + #if $override_metadata.choice == "0": + "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" + #else + "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" + #end if + "--output_format=$output_format" + </command> + + <inputs> + <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/> + <param name="output_format" type="select" format="integer" label="output format"> + <option value="fasta" selected="true">FastA format</option> + <option value="primer3">Primer3 input</option> + </param> + <conditional name="override_metadata"> + <param name="choice" type="select" format="integer" label="choose columns"> + <option value="0" selected="true">No, get columns from metadata</option> + <option value="1" >Yes, choose columns</option> + </param> + <when value="0" /> + <when value="1"> + <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/> + <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/> + <param name="species" type="select" label="Choose species"> + <options from_file="gd.species.txt"> + <column name="name" index="1"/> + <column name="value" index="0"/> + </options> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="output"/> + </outputs> + + <!-- Need snpcalls files from Webb before uncommenting + <tests> + <test> + <param name="input" value="genome_diversity/test_out/select_snps/select_snps.wsf" ftype="wsf" /> + <param name="output_format" value="primer3" /> + <param name="choice" value="0" /> + <output name="output" file="genome_diversity/test_out/extract_flanking_dna/extract_flanking_dna.txt" /> + </test> + </tests> + --> + + <help> +**What it does** + + It reports a DNA segment containing each SNP, with up to 200 nucleotides on + either side of the SNP position, which is indicated by "n". Fewer nucleotides + are reported if the SNP is near an end of the assembled genome fragment. + +----- + +**Example** + +- input file:: + + chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0 + chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 + chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 + chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 + chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 + chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 + chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0 + chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 + chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 + chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 + etc. + +- output file:: + + > chr2_75111355_75112576 314 A C + TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT + > chr8_93901796_93905612 2471 A C + GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC + > chr10_7434473_7435447 524 T C + ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC + > chr14_80021455_80022064 138 G A + ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG + > chr15_64470252_64471048 89 G A + TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT + etc. + </help> +</tool>