Mercurial > repos > rico > test_single_file
changeset 7:18dad59e1529
Uploaded
author | rico |
---|---|
date | Thu, 05 Apr 2012 15:14:25 -0400 |
parents | e521b7111644 |
children | 5f6ee4f6fd0b |
files | extract_primers.xml |
diffstat | 1 files changed, 88 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_primers.xml Thu Apr 05 15:14:25 2012 -0400 @@ -0,0 +1,88 @@ +<tool id="gd_extract_primers" name="Extract primers" version="1.0.0"> + <description>for selected SNPs</description> + + <command interpreter="python"> + extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.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 + </command> + + <inputs> + <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/> + <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> + + <tests> + <test> + <param name="input" value="genome_diversity/test_out/select_snps/select_snps.wsf" ftype="wsf" /> + <param name="choice" value="0"/> + <output name="output" file="genome_diversity/test_out/extract_primers/extract_primers.txt" /> + </test> + </tests> + + + <help> +**What it does** + + This tool extracts primers for SNPs in the dataset using the Primer3 program. + The first line of output for a given SNP reports the name of the assembled + contig, the SNP's position in the contig, the two variant nucleotides, and + Primer3's "pair penalty". The next line, if not blank, names restriction + enzymes (from the user-adjustable list) that differentially cut at that + site, but do not cut at any other position between and including the + primer positions. The next lines show the SNP's flanking regions, with + the SNP position indicated by "n", including the primer positions and an + additional 3 nucleotides. + +----- + +**Example** + +- input file:: + + chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6 + chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1 + chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4 + chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4 + +- output file:: + + chr5_30800874_30802049 734 G A 0.352964 + BglII,MboI,Sau3AI,Tru9I,XhoII + 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA + >>>>>>>>>>>>>>>>>>>> + + 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT + + + 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT + <<<<<<< + + 181 TGAACCTTGGCTCTGA + <<<<<<<<<<<<< + etc. + </help> +</tool>