Mercurial > repos > jjohnson > gmap
diff snpindex.xml @ 3:488e9d642566 draft
GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress
| author | peterjc |
|---|---|
| date | Wed, 28 Sep 2016 10:47:28 -0400 |
| parents | f6ba0f12cca2 |
| children | 14561eb803a5 |
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--- a/snpindex.xml Wed Sep 28 10:43:44 2016 -0400 +++ b/snpindex.xml Wed Sep 28 10:47:28 2016 -0400 @@ -1,77 +1,10 @@ -<tool id="gmap_snpindex" name="GMAP SNP Index" version="3.0.0"> +<tool id="gmap_snpindex" name="GMAP SNP Index" version="3.0.1"> <description>build index files for known SNPs</description> <requirements> <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> - <version_string>snpindex --version</version_string> + <version_command>snpindex --version</version_command> <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> - <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="gmapdb">Use gmapdb from the history</option> - </param> - <when value="indexed"> - <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> - <column name="uid" index="0" /> - <column name="dbkey" index="1" /> - <column name="name" index="2" /> - <column name="kmers" index="3" /> - <column name="maps" index="4" /> - <column name="snps" index="5" /> - <column name="value" index="6" /> - </options> - </param> - </when> - <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" - help="A GMAP database built with GMAP Build"/> - </when> - </conditional> - <conditional name="dbsnp"> - <param name="snp_source" type="select" label="Add SNP info from" > - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</option> - <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option> - </param> - <when value="snpTable"> - <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> - <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" /> - <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> - <option value="1" selected="true">1 (High)</option> - <option value="2">2 (Medium)</option> - <option value="3">3 (All)</option> - </param> - </when> - <when value="snpFile"> - <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file" - help="Format (3 columns): - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - <br>Each line must start with a > character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) - <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. - If the one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a probable error. - The N stands for any other allele." /> - </when> - <when value="snpIIT"> - <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" /> - </when> - </conditional> - <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters"> - </param> - </inputs> - <outputs> - <!-- - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - --> - <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" /> - </outputs> <configfiles> <configfile name="shscript"> #!/bin/bash @@ -84,7 +17,7 @@ #set $gmapdb = $refGenomeSource.gmapdb.extra_files_path #set $refname = $refGenomeSource.gmapdb.metadata.db_name #else: -#set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value) +#set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value) $refname = $os.path.basename($refGenomeSource.gmapindex.value) #end if #set $gmapsnpdir = $output.extra_files_path @@ -110,16 +43,79 @@ #end if </configfile> </configfiles> - + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="gmapdb">Use gmapdb from the history</option> + </param> + <when value="indexed"> + <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_file="gmap_indices.loc"> + <column name="uid" index="0" /> + <column name="dbkey" index="1" /> + <column name="name" index="2" /> + <column name="kmers" index="3" /> + <column name="maps" index="4" /> + <column name="snps" index="5" /> + <column name="value" index="6" /> + </options> + </param> + </when> + <when value="gmapdb"> + <param name="gmapdb" type="data" format="gmapdb" label="Select a gmapdb" + help="A GMAP database built with GMAP Build"/> + </when> + </conditional> + <conditional name="dbsnp"> + <param name="snp_source" type="select" label="Add SNP info from" > + <option value="snpTable">UCSC SNP Table</option> + <option value="snpFile">GMAP SNP File</option> + <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option> + </param> + <when value="snpTable"> + <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> + <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" /> + <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> + <option value="1" selected="true">1 (High)</option> + <option value="2">2 (Medium)</option> + <option value="3">3 (All)</option> + </param> + </when> + <when value="snpFile"> + <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file" + help="Format (3 columns): + <br>>rs62211261 21:14379270 CG + <br>>rs62211262 21:14379281 CG + <br>Each line must start with a > character, then be followed by an + identifier (which may have duplicates). Then there should be the + chromosomal coordinate of the SNP. (Coordinates are all 1-based, so + the first character of a chromosome is number 1.) Finally, there + should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) + <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. + If the one of these two letters does not match the allele in the reference + sequence, that SNP will be ignored in subsequent processing as a probable error. + The N stands for any other allele." /> + </when> + <when value="snpIIT"> + <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" /> + </when> + </conditional> + <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters"> + </param> + </inputs> + <outputs> + <!-- + <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> + --> + <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" /> + </outputs> <tests> - </tests> - + </tests> <help> - - **GMAP SNP Index** -GMAP SNP Index (snpindex in the GMAP documentaion) creates an index for known SNPs allowing for SNP tolerant mapping and alignment when using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). +GMAP SNP Index (snpindex in the GMAP documentaion) creates an index for known SNPs allowing for SNP tolerant mapping and alignment when using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). You will want to read the README_ @@ -129,8 +125,8 @@ .. _GSNAP: http://research-pub.gene.com/gmap/ .. _README: http://research-pub.gene.com/gmap/src/README .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - - </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bti310</citation> + </citations> </tool> -