gmap: snpindex.xml annotate

annotate snpindex.xml @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

author	peterjc
date	Fri, 21 Oct 2016 10:55:40 -0400
parents	488e9d642566
children

rev	line source
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	1 <tool id="gmap_snpindex" name="GMAP SNP Index" version="3.0.1">
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	2 <description>build index files for known SNPs</description>
10e3476429b5 Uploaded jjohnson parents: diff changeset	3 <requirements>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	4 <requirement type="package" version="2013-05-09">gmap</requirement>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	5 </requirements>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	6 <version_command>snpindex --version</version_command>
5 14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	7 <command detect_errors="exit_code" interpreter="bash"><![CDATA[
14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	8 $shscript 2>1 1> $output
14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	9 ]]></command>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	10 <configfiles>
5 14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	11 <configfile name="shscript"><![CDATA[
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	12 #!/bin/bash
10e3476429b5 Uploaded jjohnson parents: diff changeset	13 #set $ds = chr(36)
10e3476429b5 Uploaded jjohnson parents: diff changeset	14 #set $gt = chr(62)
10e3476429b5 Uploaded jjohnson parents: diff changeset	15 #set $lt = chr(60)
10e3476429b5 Uploaded jjohnson parents: diff changeset	16 #set $ad = chr(38)
10e3476429b5 Uploaded jjohnson parents: diff changeset	17 #import os.path
10e3476429b5 Uploaded jjohnson parents: diff changeset	18 #if $refGenomeSource.genomeSource == "gmapdb":
10e3476429b5 Uploaded jjohnson parents: diff changeset	19 #set $gmapdb = $refGenomeSource.gmapdb.extra_files_path
10e3476429b5 Uploaded jjohnson parents: diff changeset	20 #set $refname = $refGenomeSource.gmapdb.metadata.db_name
10e3476429b5 Uploaded jjohnson parents: diff changeset	21 #else:
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	22 #set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value)
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	23 $refname = $os.path.basename($refGenomeSource.gmapindex.value)
10e3476429b5 Uploaded jjohnson parents: diff changeset	24 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	25 #set $gmapsnpdir = $output.extra_files_path
10e3476429b5 Uploaded jjohnson parents: diff changeset	26 mkdir -p $gmapsnpdir
10e3476429b5 Uploaded jjohnson parents: diff changeset	27 #set $snpsname = $snps_name.__str__
10e3476429b5 Uploaded jjohnson parents: diff changeset	28 #set $snpsiit = '.'.join([$snpsname,'iit'])
10e3476429b5 Uploaded jjohnson parents: diff changeset	29 #set $pathsnps = $os.path.join($gmapsnpdir,$snpsname)
10e3476429b5 Uploaded jjohnson parents: diff changeset	30 #set $pathsnpsiit = $os.path.join($gmapsnpdir,$snpsiit)
10e3476429b5 Uploaded jjohnson parents: diff changeset	31 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	32 #if $dbsnp.snp_source == 'snpTable':
10e3476429b5 Uploaded jjohnson parents: diff changeset	33 #if $dbsnp.snpsex.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	34 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex \| iit_store -o $pathsnps
10e3476429b5 Uploaded jjohnson parents: diff changeset	35 #else:
10e3476429b5 Uploaded jjohnson parents: diff changeset	36 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight \| iit_store -o $pathsnps
10e3476429b5 Uploaded jjohnson parents: diff changeset	37 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	38 #elif $dbsnp.snp_source == 'snpFile':
10e3476429b5 Uploaded jjohnson parents: diff changeset	39 cat $dbsnp.snps \| iit_store -o $pathsnps
10e3476429b5 Uploaded jjohnson parents: diff changeset	40 #elif $dbsnp.snp_source == 'snpIIT':
10e3476429b5 Uploaded jjohnson parents: diff changeset	41 cat $dbsnp.snps > $pathsnpsiit
10e3476429b5 Uploaded jjohnson parents: diff changeset	42 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	43 snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
10e3476429b5 Uploaded jjohnson parents: diff changeset	44 echo snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
10e3476429b5 Uploaded jjohnson parents: diff changeset	45 #end if
5 14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	46 ]]></configfile>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	47 </configfiles>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	48 <inputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	49 <conditional name="refGenomeSource">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	50 <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">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	51 <option value="indexed">Use a built-in index</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	52 <option value="gmapdb">Use gmapdb from the history</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	53 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	54 <when value="indexed">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	55 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
5 14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	56 <options from_data_table="gmap_indices">
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	57 <column name="uid" index="0" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	58 <column name="dbkey" index="1" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	59 <column name="name" index="2" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	60 <column name="kmers" index="3" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	61 <column name="maps" index="4" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	62 <column name="snps" index="5" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	63 <column name="value" index="6" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	64 </options>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	65 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	66 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	67 <when value="gmapdb">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	68 <param name="gmapdb" type="data" format="gmapdb" label="Select a gmapdb"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	69 help="A GMAP database built with GMAP Build"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	70 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	71 </conditional>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	72 <conditional name="dbsnp">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	73 <param name="snp_source" type="select" label="Add SNP info from" >
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	74 <option value="snpTable">UCSC SNP Table</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	75 <option value="snpFile">GMAP SNP File</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	76 <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	77 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	78 <when value="snpTable">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	79 <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	80 <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" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	81 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	82 <option value="1" selected="true">1 (High)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	83 <option value="2">2 (Medium)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	84 <option value="3">3 (All)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	85 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	86 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	87 <when value="snpFile">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	88 <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	89 help="Format (3 columns):
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	90 <br>>rs62211261 21:14379270 CG
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	91 <br>>rs62211262 21:14379281 CG
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	92 <br>Each line must start with a > character, then be followed by an
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	93 identifier (which may have duplicates). Then there should be the
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	94 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	95 the first character of a chromosome is number 1.) Finally, there
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	96 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	97 <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome.
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	98 If the one of these two letters does not match the allele in the reference
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	99 sequence, that SNP will be ignored in subsequent processing as a probable error.
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	100 The N stands for any other allele." />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	101 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	102 <when value="snpIIT">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	103 <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	104 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	105 </conditional>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	106 <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	107 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	108 </inputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	109 <outputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	110 <!--
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	111 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	112 -->
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	113 <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	114 </outputs>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	115 <tests>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	116 </tests>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	117 <help>
10e3476429b5 Uploaded jjohnson parents: diff changeset	118 GMAP SNP Index
10e3476429b5 Uploaded jjohnson parents: diff changeset	119
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	120 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).
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	121
10e3476429b5 Uploaded jjohnson parents: diff changeset	122 You will want to read the README_
10e3476429b5 Uploaded jjohnson parents: diff changeset	123
10e3476429b5 Uploaded jjohnson parents: diff changeset	124 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
10e3476429b5 Uploaded jjohnson parents: diff changeset	125
10e3476429b5 Uploaded jjohnson parents: diff changeset	126 .. _GMAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	127 .. _GSNAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	128 .. _README: http://research-pub.gene.com/gmap/src/README
10e3476429b5 Uploaded jjohnson parents: diff changeset	129 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
10e3476429b5 Uploaded jjohnson parents: diff changeset	130 </help>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	131 <citations>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	132 <citation type="doi">10.1093/bioinformatics/bti310</citation>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	133 </citations>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	134 </tool>

Mercurial > repos > jjohnson > gmap

annotate snpindex.xml @ 5:14561eb803a5 draft