Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 13:42f1509f3d5a draft

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author yating-l
date Fri, 12 May 2017 12:06:17 -0400
parents 61e2768506c1
children 275949b792a4
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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 $noHead == "yes"
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10 -noHead
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11 #end if
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12 -q=$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 ]]></command>
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20 <inputs>
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21 <conditional name="reference_source">
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22 <param name="reference_source_selector" type="select" label="Choose the source for the database">
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23 <option value="cached">Locally cached</option>
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24 <option value="history">History</option>
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25 </param>
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26 <when value="cached">
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27 <param name="database" type="select" label="Select database">
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28 <options from_data_table="all_fasta">
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29 </options>
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30 <validator type="no_options" message="A built-in database is not available" />
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31 </param>
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32 </when>
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33 <when value="history">
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34 <param name="database" type="data" format="fasta" label="Using database file" />
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35 </when>
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36 </conditional>
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37 <param type="data" name="query" format="fasta" />
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38 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
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39 <option value="dna">dna - DNA sequence</option>
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40 <option value="prot">prot - protein sequence</option>
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41 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
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42 </param>
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43 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
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44 <option value="dna">dna - DNA sequence </option>
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45 <option value="rna">rna - RNA sequence</option>
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46 <option value="prot">prot - protein sequence</option>
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47 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
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48 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
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49 </param>
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50 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
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51 <option value="yes" selected="true">Yes, suppresses .psl header</option>
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52 <option value="no">No, do not suppresses .psl header</option>
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53 </param>
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54 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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55 but may extend through it in nucleotide searches. Masked areas
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56 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
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57 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
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58 <option value="upper">upper - mask out upper-cased sequence</option>
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59 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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60 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="reference_source_selector" value="history" />
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69 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
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70 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
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71 <param name="database_type" value="dnax" />
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72 <param name="query_type" value="rnax" />
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73 <param name="noHead" value="yes" />
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74 <param name="mask" value="lower" />
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75 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
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76 </test>
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77 <test>
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78 <param name="reference_source_selector" value="history" />
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79 <param name="database" value="dbia3/dbia3.fa" />
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80 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
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81 <param name="database_type" value="dnax" />
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82 <param name="query_type" value="rnax" />
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83 <param name="noHead" value="yes" />
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84 <param name="mask" value="lower" />
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85 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
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86 </test>
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87
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88 </tests>
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89 <help>
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90 <![CDATA[
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91 BLAT
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92 ====
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93 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
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94
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95 blat (version: v340)- Standalone blat sequence search command line tool.
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96 -------------------------------------------------------------------------
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97
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98 usage:
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99 ++++++
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100
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101 $ blat database query [-ooc=11.ooc] output.psl
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102
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103 where:
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104 database and query are each either a .fa, .nib or .2bit file,
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105 or a list of these files with one file name per line.
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106 -ooc=11.ooc tells the program to load over-occurring 11-mers from
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107 an external file. This will increase the speed
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108 by a factor of 40 in many cases, but is not required.
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109 output.psl is the name of the output file.
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110
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111 documentation:
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112 ++++++++++++++
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113
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114 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
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115
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116 Source code:
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117 ++++++++++++
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118
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119 http://hgdownload.cse.ucsc.edu/admin/exe/
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120
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121 ]]></help>
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122 <citations>
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123 <citation type="bibtex">@article{kent2002blat,
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124 title={BLAT—the BLAST-like alignment tool},
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125 author={Kent, W James},
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126 journal={Genome research},
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127 volume={12},
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128 number={4},
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129 pages={656--664},
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130 year={2002},
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131 publisher={Cold Spring Harbor Lab}
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132 }</citation>
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133 </citations>
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134 </tool>
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