Mercurial > repos > jjohnson > gmap
annotate gmap/gmap_build.xml @ 2:52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Oct 2011 11:38:55 -0500 |
| parents | d58d272914e7 |
| children |
| rev | line source |
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| 0 | 1 <tool id="gmap_build" name="GMAP Build" version="2.0.0"> |
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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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2 <description>a database genome index for GMAP and GSNAP</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="binary">gmap_build</requirement> | |
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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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5 <!-- proposed tag for added datatype dependencies --> |
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52da588232b0
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6 <requirement type="datatype">gmapdb</requirement> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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7 <requirement type="datatype">gmap_snps</requirement> |
| 0 | 8 </requirements> |
| 9 <version_string>gmap --version</version_string> | |
| 10 <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> | |
| 11 <inputs> | |
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12 <!-- Name for this gmapdb --> |
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13 <param name="refname" type="text" label="Name you want to give this gmap database" help=""> |
| 0 | 14 <validator type="empty_field" message="A database name is required."/> |
| 15 </param> | |
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16 <!-- Input data --> |
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17 <repeat name="inputs" title="Reference Sequence" min="1"> |
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18 <param name="input" type="data" format="fasta" label="reference sequence fasta" /> |
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19 </repeat> |
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52da588232b0
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20 |
| 0 | 21 <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help=""> |
| 22 <option value="12">12</option> | |
| 23 <option value="13">13</option> | |
| 24 <option value="14">14</option> | |
| 25 <option value="15" selected="true">15</option> | |
| 26 </param> | |
| 27 <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/> | |
| 28 <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/> | |
| 29 <conditional name="splicesite"> | |
| 30 <param name="splice_source" type="select" label="Add splice and intron info from" > | |
| 31 <option value="none"></option> | |
| 32 <option value="refGeneTable">refGenes table from UCSC table browser</option> | |
| 33 <option value="gtf">GTF</option> | |
| 34 <option value="gff3">GFF3</option> | |
| 35 </param> | |
| 36 <when value="none"/> | |
| 37 <when value="refGeneTable"> | |
| 38 <param name="refGenes" type="data" format="tabular" optional="true" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" /> | |
| 39 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" | |
| 40 help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> | |
| 41 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> | |
| 42 </param> | |
| 43 | |
| 44 </when> | |
| 45 <when value="gtf"> | |
| 46 <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" /> | |
| 47 </when> | |
| 48 <when value="gff3"> | |
| 49 <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" /> | |
| 50 </when> | |
| 51 </conditional> | |
| 52 <conditional name="dbsnp"> | |
| 53 <param name="snp_source" type="select" label="Add SNP info from" > | |
| 54 <option value="none"></option> | |
| 55 <option value="snpTable">UCSC SNP Table</option> | |
| 56 <option value="snpFile">GMAP SNP File</option> | |
| 57 </param> | |
| 58 <when value="none"/> | |
| 59 <when value="snpTable"> | |
| 60 <param name="snps" type="data" format="tabular" optional="true" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> | |
| 61 <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" /> | |
| 62 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> | |
| 63 <option value="1" selected="true">1 (High)</option> | |
| 64 <option value="2">2 (Medium)</option> | |
| 65 <option value="3">3 (All)</option> | |
| 66 </param> | |
| 67 </when> | |
| 68 <when value="snpFile"> | |
| 69 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" | |
| 70 help="Format (3 columns): | |
| 71 <br>>rs62211261 21:14379270 CG | |
| 72 <br>>rs62211262 21:14379281 CG | |
| 73 <br>Each line must start with a > character, then be followed by an | |
| 74 identifier (which may have duplicates). Then there should be the | |
| 75 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so | |
| 76 the first character of a chromosome is number 1.) Finally, there | |
| 77 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) | |
| 78 <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. | |
| 79 If the one of these two letters does not match the allele in the reference | |
| 80 sequence, that SNP will be ignored in subsequent processing as a probable error. | |
| 81 The N stands for any other allele." /> | |
| 82 </when> | |
| 83 </conditional> | |
| 84 </inputs> | |
| 85 <outputs> | |
| 86 <!-- | |
| 87 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> | |
| 88 --> | |
| 89 <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" /> | |
| 90 </outputs> | |
| 91 <configfiles> | |
| 92 <configfile name="shscript"> | |
| 93 #!/bin/bash | |
| 94 #set $ds = chr(36) | |
| 95 #set $gt = chr(62) | |
| 96 #set $lt = chr(60) | |
| 97 #set $ad = chr(38) | |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
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98 ## #set $ref_files = '' |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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parents:
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99 ## #for $i in $inputs: |
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52da588232b0
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parents:
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100 ## #set $ref_files = $ref_files $i.input |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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parents:
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101 ## #end for |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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parents:
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102 ## echo $ref_files |
| 0 | 103 #import os.path |
| 104 #set $gmapdb = $output.extra_files_path | |
| 105 #set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps') | |
| 106 mkdir -p $gmapdb | |
| 107 ## export GMAPDB required for cmetindex and atoiindex | |
| 108 export GMAPDB=$gmapdb | |
| 109 #for $k in $kmer.__str__.split(','): | |
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110 gmap_build -D $gmapdb -d $refname -s numeric-alpha -k $k #for i in $inputs# ${i.input}#end for# |
| 0 | 111 #end for |
| 112 get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /' | |
| 113 echo "kmers: " $kmer | |
| 114 #if $splicesite.splice_source == 'refGeneTable': | |
| 115 #if $splicesite.refGenes.__str__ != 'None': | |
| 116 cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'splicesites') | |
| 117 cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'introns') | |
| 118 #end if | |
| 119 #elif $splicesite.splice_source == 'gtf': | |
| 120 #if $splicesite.gtfGenes.__str__ != 'None': | |
| 121 cat $splicesite.gtfGenes | gtf_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites') | |
| 122 cat $splicesite.gtfGenes | gtf_introns | iit_store -o $os.path.join($mapsdir,'introns') | |
| 123 #end if | |
| 124 #elif $splicesite.splice_source == 'gff3': | |
| 125 #if $splicesite.gff3Genes.__str__ != 'None': | |
| 126 cat $splicesite.gff3Genes | gff3_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites') | |
| 127 cat $splicesite.gff3Genes | gff3_introns | iit_store -o $os.path.join($mapsdir,'introns') | |
| 128 #end if | |
| 129 #end if | |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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130 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None': |
| 0 | 131 #if $dbsnp.snp_source == 'snpTable': |
| 132 #if $dbsnp.snpsex.__str__ != 'None': | |
| 133 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $os.path.join($mapsdir,'snps') | |
| 134 #else: | |
| 135 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $os.path.join($mapsdir,'snps') | |
| 136 #end if | |
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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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137 #else: |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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138 cat $dbsnp.snps | iit_store -o $os.path.join($mapsdir,'snps') |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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139 #end if |
| 0 | 140 snpindex -d $refname -v snps |
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141 echo "snpindex" -d $refname -v snps |
| 0 | 142 #end if |
| 143 #if $cmetindex.__str__ == 'yes': | |
| 144 cmetindex -d $refname | |
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145 echo "cmetindex" -d $refname |
| 0 | 146 #end if |
| 147 #if $atoiindex.__str__ == 'yes': | |
| 148 atoiindex -d $refname | |
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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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149 echo "atoiindex" -d $refname |
| 0 | 150 #end if |
| 151 get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' | |
| 152 </configfile> | |
| 153 </configfiles> | |
| 154 | |
| 155 <tests> | |
| 156 </tests> | |
| 157 | |
| 158 <help> | |
| 159 | |
| 160 | |
| 161 **GMAP Build** | |
| 162 | |
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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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163 GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). (GMAP Build uses GMSP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.) |
| 0 | 164 |
| 165 You will want to read the README_ | |
| 166 | |
| 167 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 | |
| 168 | |
| 169 .. _GMAP: http://research-pub.gene.com/gmap/ | |
| 170 .. _GSNAP: http://research-pub.gene.com/gmap/ | |
| 171 .. _README: http://research-pub.gene.com/gmap/src/README | |
| 172 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 | |
| 173 | |
| 174 | |
| 175 </help> | |
| 176 </tool> | |
| 177 |