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annotate iit_store.xml @ 4:a88571642c6e draft

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Uploaded v3.0.1 again without unwanted tar-ball present.
author peterjc
date Wed, 28 Sep 2016 10:49:02 -0400
parents 488e9d642566
children 14561eb803a5
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1 <tool id="gmap_iit_store" name="GMAP IIT" version="3.0.1">
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2 <description>Create a map store for known genes or SNPs</description>
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3 <requirements>
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4 <requirement type="package" version="2013-05-09">gmap</requirement>
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5 </requirements>
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6 <version_command>iit_store --version</version_command>
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7 <command interpreter="command"> /bin/bash $shscript 2> $log </command>
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8 <configfiles>
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9 <configfile name="shscript">
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10 #!/bin/bash
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11 #set $catcmd = 'gzcat -f'
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12 #set $catcmd = 'cat'
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13 #set $ds = chr(36)
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14 #set $gt = chr(62)
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15 #set $lt = chr(60)
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16 #set $ad = chr(38)
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17 #set $ep = chr(33)
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18 #set $toerr = ''.join([$gt,$ad,'2'])
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19 #import os.path
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20 #if $map.type == 'genes':
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21 if [ $ep -e $map.src.genes ]; then echo "$map.src.genes does not exist" $toerr; exit 1; fi
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22 if [ $ep -s $map.src.genes ]; then echo "$map.src.genes is empty" $toerr; exit 2; fi
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23 #if $map.src.src_format == 'refGeneTable':
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24 #if 'splicesites' in [ $map.maps.__str__ ]:
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25 $catcmd $map.src.genes | psl_splicesites -s $map.src.col_skip | iit_store -o $splicesites_iit
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26 #end if
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27 #if 'introns' in [ $map.maps.__str__ ]:
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28 $catcmd $map.src.genes | psl_introns -s $map.src.col_skip | iit_store -o $introns_iit
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29 #end if
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30 #elif $map.src.src_format == 'gtf':
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31 #if 'splicesites' in [ $map.maps.__str__ ]:
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32 $catcmd $map.src.genes | gtf_splicesites | iit_store -o $splicesites_iit
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33 #end if
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34 #if 'introns' in [ $map.maps.__str__ ]:
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35 $catcmd $map.src.genes | gtf_introns | iit_store -o $introns_iit
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36 #end if
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37 #elif $map.src.src_format == 'gff3':
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38 #if 'splicesites' in [ $map.maps.__str__ ]:
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39 $catcmd $map.src.genes | gff3_splicesites | iit_store -o $splicesites_iit
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40 #end if
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41 #if 'introns' in [ $map.maps.__str__ ]:
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42 $catcmd $map.src.genes | gff3_introns | iit_store -o $introns_iit
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43 #end if
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44 #end if
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45 #elif $map.type == 'snps':
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46 if [ $ep -s $map.src.snps ]; then echo "$map.src.snps is empty" $toerr; exit 2; fi
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47 #if $map.src.snpsex.__str__ != 'None':
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48 $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o $snps_iit
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49 #else:
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50 $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit
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51 #end if
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52 #else:
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53 $catcmd $map.src.snps | iit_store -o $map_iit
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54 #end if
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55 </configfile>
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56 </configfiles>
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57 <inputs>
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58 <!-- Input data -->
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59 <conditional name="map">
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60 <param name="type" type="select" label="Make map for" >
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61 <option value="genes">Introns and Splice sites</option>
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62 <option value="snps">SNPs</option>
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63 <option value="gmap">GMAP Annotation</option>
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64 </param>
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65 <when value="genes">
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66 <conditional name="src">
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67 <param name="src_format" type="select" label="Add splice and intron info from" >
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68 <option value="refGeneTable">refGenes table from UCSC table browser</option>
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69 <option value="gtf">GTF</option>
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70 <option value="gff3">GFF3</option>
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71 </param>
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72 <when value="refGeneTable">
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73 <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
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74 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)"
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75 help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
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76 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
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77 </param>
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78 </when>
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79 <when value="gtf">
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80 <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" />
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81 </when>
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82 <when value="gff3">
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83 <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" />
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84 </when>
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85 </conditional>
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86 <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" >
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87 <option value="splicesites" selected="true">splicesites.iit</option>
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88 <option value="introns" selected="false">introns.iit</option>
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89 </param>
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90 </when>
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91 <when value="snps">
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92 <conditional name="src">
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93 <param name="src_format" type="select" label="Add SNP info from" >
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94 <option value="snpTable">UCSC SNP Table</option>
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95 <option value="snpFile">GMAP SNP File</option>
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96 </param>
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97 <when value="snpTable">
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98 <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
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99 <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" />
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100 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
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101 <option value="1" selected="true">1 (High)</option>
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102 <option value="2">2 (Medium)</option>
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103 <option value="3">3 (All)</option>
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104 </param>
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105 </when>
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106 <when value="snpFile">
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107 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file"
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108 help="Format (3 columns):&lt;B&gt;
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109 &lt;br&gt;>rs62211261 21:14379270 CG
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110 &lt;br&gt;>rs62211262 21:14379281 CG
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111 &lt;/B&gt;
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112 &lt;br&gt;Each line must start with a &gt; character, then be followed by an
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113 identifier (which may have duplicates). Then there should be the
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114 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
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115 the first character of a chromosome is number 1.) Finally, there
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116 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
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117 &lt;br&gt;These alleles must correspond to the possible nucleotides on the plus strand of the genome.
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118 If the one of these two letters does not match the allele in the reference
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119 sequence, that SNP will be ignored in subsequent processing as a probable error.
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120 The N stands for any other allele." />
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121 </when>
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122 </conditional>
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123 </when>
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124 <when value="gmap">
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125 <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile"
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126 help="Format (2 or columns): &lt;B&gt;
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127 &lt;br&gt;>label coords optional_tag
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128 &lt;br&gt;optional_annotation (which may be zero, one, or multiple lines)
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129 &lt;/B&gt;
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130 &lt;br&gt;Each line must start with a &gt; character, then be followed by an identifier (which may have duplicates).
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131 &lt;br&gt;Then there should be the chromosomal coordinate range. (Coordinates are all 1-based, so the first character of a chromosome is number 1.)
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132 &lt;br&gt;The coords should be of the form
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133 &lt;br&gt; chr:position
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134 &lt;br&gt; chr:startposition..endposition
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135 &lt;br&gt;The term chr:position is equivalent to chr:position..position.
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136 &lt;br&gt;If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition.
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137 " />
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138 </when>
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139 </conditional>
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140 </inputs>
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141 <outputs>
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142 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
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143 <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit">
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144 <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter>
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145 </data>
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146 <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit">
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147 <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter>
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148 </data>
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149 <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit">
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150 <filter>(map['type'] == 'snps')</filter>
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151 </data>
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152 <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit">
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153 <filter>(map['type'] == 'gmap')</filter>
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154 </data>
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155 </outputs>
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156 <tests>
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157 </tests>
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158
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159 <help>
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160
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161
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162 **iit_store**
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163
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164 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.
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165
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166 You will want to read the README_
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167
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168 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
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169
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170 .. _GMAP: http://research-pub.gene.com/gmap/
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171 .. _GSNAP: http://research-pub.gene.com/gmap/
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172 .. _README: http://research-pub.gene.com/gmap/src/README
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173 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
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174
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175
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176 **inputs**
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177
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178 </help>
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179 <citations>
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180 <citation type="doi">10.1093/bioinformatics/bti310</citation>
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181 </citations>
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182 </tool>
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183