Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 5:70d7377d5e24 draft

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planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
author yating-l
date Wed, 01 Feb 2017 17:16:02 -0500
parents 9e56efe1c371
children 6f06b6d68c0b
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1 <?xml version="1.0"?>
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2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
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3 <description>Standalone blat sequence search command line tool</description>
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4 <requirements>
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5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 blat
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9 #if $noHead
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10 -noHead
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11 #end if
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12 -q=$query_type
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13 -t=$database_type
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14 -mask=$mask
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15 '${database}'
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16 '${query}'
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17 output
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18 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
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19 && pslReps -minAli=0.25 '${output_sorted}' output.reps.psl output.reps.psr
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20 && faPolyASizes '${query}' query.polyA
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21 #if $filter_param.filter =="yes"
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22 && pslCDnaFilter
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23 #if $filter_param.assembly_type == "native"
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24 -localNearBest=0.001
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25 #if $filter_param.assembly_category == "finished"
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26 -minId=0.95
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27 -minCover=0.25
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28 #else if $filter_param.assembly_category == "well-ordered"
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29 -minId=0.95
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30 -minCover=0.15
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31 #else
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32 -minId=0.94
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33 -minAlnSize=80
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34 #end if
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35 #else
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36 -localNearBest=0.010
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37 #if $filter_param.assembly_category == "finished"
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38 -minId=0.35
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39 -minCover=0.25
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40 #else if $filter_param.assembly_category == "well-ordered"
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41 -minId=0.35
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42 -minCover=0.15
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43 #else
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44 -minId=0.33
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45 -minAlnSize=80
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46 #end if
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47 #end if
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48 -minQSize=20
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49 -ignoreIntrons
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50 -repsAsMatch
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51 -ignoreNs
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52 -bestOverlap
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53 -polyASizes=query.polyA
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54 output.reps.psl
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55 '${output_filtered}'
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56 #end if
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57 ]]></command>
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58 <inputs>
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59 <param type="data" name="database" format="fasta" />
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60 <param type="data" name="query" format="fasta" />
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61 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dna">
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62 <option value="dna">DNA sequence</option>
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63 <option value="prot">protein sequence</option>
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64 <option value="dnax">DNA sequence translated in six frames to protein</option>
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65 </param>
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66 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is dna">
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67 <option value="dna">DNA sequence</option>
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68 <option value="rna">RNA sequence</option>
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69 <option value="prot">protein sequence</option>
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70 <option value="dnax">DNA sequence translated in six frames to protein</option>
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71 <option value="rnax">DNA sequence translated in three frames to protein</option>
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72 </param>
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73 <param name="noHead" type="boolean" value="false" label="Suppresses .psl header (so it's just a tab-separated file)." />
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74 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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75 but may extend through it in nucleotide searches. Masked areas
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76 are ignored entirely in protein or translated searches.">
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77 <option value="lower">lower - mask out lower-cased sequence</option>
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78 <option value="upper">upper - mask out upper-cased sequence</option>
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79 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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80 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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81 </param>
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82 <conditional name="filter_param">
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83 <param name="filter" type="select" label="Filter BLAT results with pslCDnaFilter">
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84 <option value="no" selected="true">No</option>
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85 <option value="yes">Yes</option>
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86 </param>
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87 <when value="yes">
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88 <param name="assembly_type" type="select" label="Choose your type of cDNA sequence">
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89 <option value="native">Same species</option>
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90 <option value="xeno">Across species</option>
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91 </param>
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92 <param name="assembly_category" type="select" label="Choose your genome assembly category">
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93 <option value="finished">finished assemblies (high quality)</option>
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94 <option value="well-ordered">well-ordered assemblies (well ordered, whole genome shotgun)</option>
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95 <option value="low-coverage">low-coverage assemblies (low coverage (&lt; 4x"), lots of contigs, N50 scaffold size &lt; 1mb) </option>
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96 </param>
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97 </when>
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98 </conditional>
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99 </inputs>
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100 <outputs>
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101 <data format="psl" name="output_sorted"></data>
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102 <data format="psl" name="output_filtered"></data>
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="database" value="amaVit1.fa" />
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107 <param name="query" value="Gallus_gallus_RefSeq.fa" />
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108 <param name="database_type" value="dnax" />
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109 <param name="query_type" value="rnax" />
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110 <param name="noHead" value="true" />
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111 <param name="mask" value="lower" />
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112 <param name="filter" value="yes" />
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113 <param name="assembly_type" value="xeno" />
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114 <param name="assembly_category" value="well-ordered" />
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115 <output name="output_sorted" value="amaVit1_Gallus_gallus.psl" />
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116 <output name="output_filtered" value="amaVit1_Gallus_gallus_filtered.psl" />
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117 </test>
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118 </tests>
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119 <help>
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120 <![CDATA[
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121 BLAT
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122 ====
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123 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
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124
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125 blat (version: v340)- Standalone blat sequence search command line tool.
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126 ---------------------------------------------------------
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127 usage:
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128 ++++++
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129 blat database query [-ooc=11.ooc] output.psl
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130 where:
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131 database and query are each either a .fa, .nib or .2bit file,
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132 or a list of these files with one file name per line.
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133 -ooc=11.ooc tells the program to load over-occurring 11-mers from
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134 an external file. This will increase the speed
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135 by a factor of 40 in many cases, but is not required.
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136 output.psl is the name of the output file.
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137 documentation:
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138 ++++++++++++++
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139 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
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140 Source code:
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141 ++++++++++++
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142 http://hgdownload.cse.ucsc.edu/admin/exe/
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143 pslCDnaFilter (version: v340)
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144 ---------------------------
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145 Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
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146 usage:
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147 ++++++
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148 pslCDnaFilter [options] inPsl outPsl
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149 Source code:
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150 ++++++++++++
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151 http://hgdownload.cse.ucsc.edu/admin/exe/
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152
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153 Licence
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154 =======
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155 Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).
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156 ]]>
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157 </help>
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158 <citations>
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159 <citation type="bibtex">@article{kent2002blat,
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160 title={BLAT—the BLAST-like alignment tool},
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161 author={Kent, W James},
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162 journal={Genome research},
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163 volume={12},
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164 number={4},
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165 pages={656--664},
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166 year={2002},
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167 publisher={Cold Spring Harbor Lab}
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168 }</citation>
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169 </citations>
0
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170 </tool>
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171
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172
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173
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174
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175