Mercurial > repos > jjohnson > gmap
diff iit_store.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/iit_store.xml Wed Sep 28 10:43:44 2016 -0400 +++ b/iit_store.xml Wed Sep 28 10:47:28 2016 -0400 @@ -1,109 +1,10 @@ -<tool id="gmap_iit_store" name="GMAP IIT" version="3.0.0"> +<tool id="gmap_iit_store" name="GMAP IIT" version="3.0.1"> <description>Create a map store for known genes or SNPs</description> <requirements> <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> - <version_string>iit_store --version</version_string> + <version_command>iit_store --version</version_command> <command interpreter="command"> /bin/bash $shscript 2> $log </command> - <inputs> - <!-- Input data --> - <conditional name="map"> - <param name="type" type="select" label="Make map for" > - <option value="genes">Introns and Splice sites</option> - <option value="snps">SNPs</option> - <option value="gmap">GMAP Annotation</option> - </param> - <when value="genes"> - <conditional name="src"> - <param name="src_format" type="select" label="Add splice and intron info from" > - <option value="refGeneTable">refGenes table from UCSC table browser</option> - <option value="gtf">GTF</option> - <option value="gff3">GFF3</option> - </param> - <when value="refGeneTable"> - <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" /> - <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" - help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> - <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> - </param> - </when> - <when value="gtf"> - <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" /> - </when> - <when value="gff3"> - <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" /> - </when> - </conditional> - <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" > - <option value="splicesites" selected="true">splicesites.iit</option> - <option value="introns" selected="false">introns.iit</option> - </param> - </when> - <when value="snps"> - <conditional name="src"> - <param name="src_format" type="select" label="Add SNP info from" > - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</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" optional="true" label="GMAP SNPs file" - help="Format (3 columns):<B> - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - </B> - <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> - </conditional> - </when> - <when value="gmap"> - <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile" - help="Format (2 or columns): <B> - <br>>label coords optional_tag - <br>optional_annotation (which may be zero, one, or multiple lines) - </B> - <br>Each line must start with a > character, then be followed by an identifier (which may have duplicates). - <br>Then there should be the chromosomal coordinate range. (Coordinates are all 1-based, so the first character of a chromosome is number 1.) - <br>The coords should be of the form - <br> chr:position - <br> chr:startposition..endposition - <br>The term chr:position is equivalent to chr:position..position. - <br>If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition. - " /> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit"> - <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter> - </data> - <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit"> - <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter> - </data> - <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit"> - <filter>(map['type'] == 'snps')</filter> - </data> - <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit"> - <filter>(map['type'] == 'gmap')</filter> - </data> - </outputs> <configfiles> <configfile name="shscript"> #!/bin/bash @@ -146,23 +47,121 @@ #if $map.src.snpsex.__str__ != 'None': $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o $snps_iit #else: - $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit + $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit #end if #else: - $catcmd $map.src.snps | iit_store -o $map_iit + $catcmd $map.src.snps | iit_store -o $map_iit #end if </configfile> </configfiles> - + <inputs> + <!-- Input data --> + <conditional name="map"> + <param name="type" type="select" label="Make map for" > + <option value="genes">Introns and Splice sites</option> + <option value="snps">SNPs</option> + <option value="gmap">GMAP Annotation</option> + </param> + <when value="genes"> + <conditional name="src"> + <param name="src_format" type="select" label="Add splice and intron info from" > + <option value="refGeneTable">refGenes table from UCSC table browser</option> + <option value="gtf">GTF</option> + <option value="gff3">GFF3</option> + </param> + <when value="refGeneTable"> + <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" /> + <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" + help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> + <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> + </param> + </when> + <when value="gtf"> + <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" /> + </when> + <when value="gff3"> + <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" /> + </when> + </conditional> + <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" > + <option value="splicesites" selected="true">splicesites.iit</option> + <option value="introns" selected="false">introns.iit</option> + </param> + </when> + <when value="snps"> + <conditional name="src"> + <param name="src_format" type="select" label="Add SNP info from" > + <option value="snpTable">UCSC SNP Table</option> + <option value="snpFile">GMAP SNP File</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" optional="true" label="GMAP SNPs file" + help="Format (3 columns):<B> + <br>>rs62211261 21:14379270 CG + <br>>rs62211262 21:14379281 CG + </B> + <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> + </conditional> + </when> + <when value="gmap"> + <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile" + help="Format (2 or columns): <B> + <br>>label coords optional_tag + <br>optional_annotation (which may be zero, one, or multiple lines) + </B> + <br>Each line must start with a > character, then be followed by an identifier (which may have duplicates). + <br>Then there should be the chromosomal coordinate range. (Coordinates are all 1-based, so the first character of a chromosome is number 1.) + <br>The coords should be of the form + <br> chr:position + <br> chr:startposition..endposition + <br>The term chr:position is equivalent to chr:position..position. + <br>If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition. + " /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> + <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit"> + <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter> + </data> + <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit"> + <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter> + </data> + <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit"> + <filter>(map['type'] == 'snps')</filter> + </data> + <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit"> + <filter>(map['type'] == 'gmap')</filter> + </data> + </outputs> <tests> - </tests> + </tests> <help> **iit_store** -GMAP IIT creates an Interval Index Tree map of known splice sites, introns, or SNPs (it uses iit_store described in the GMAP documentation). The maps can be used in GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). Maps are typically used for known splice sites, introns, or SNPs. +GMAP IIT creates an Interval Index Tree map of known splice sites, introns, or SNPs (it uses iit_store described in the GMAP documentation). The maps can be used in GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). Maps are typically used for known splice sites, introns, or SNPs. You will want to read the README_ @@ -177,5 +176,8 @@ **inputs** </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bti310</citation> + </citations> </tool>