Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 23:1d17fb76718e draft

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planemo upload commit c6e5cf60eae0c793f7186b7414a0714a14f5c0e7-dirty
author yating-l
date Tue, 23 May 2017 18:27:21 -0400
parents 93159496f9c0
children 4faaa87eca43
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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 #if str($reference_source.reference_source_selector) == "history":
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9 #set $reference_fasta_filename = "localref.fa"
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10 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
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11 #else:
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12 #set $reference_fasta_filename = str($reference_source.database.fields.path)
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13 #end if
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14 blat
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15 #if $noHead == "yes"
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16 -noHead
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17 #end if
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18 -q=$query_type
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19 -t=$database_type
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20 #if $mask_type.mask == "file.out":
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21 -mask=$mask_type.mask_file
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22 #else:
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23 -mask=$mask_type.mask
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24 #end if
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25 '$reference_fasta_filename'
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26 '${query}'
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27 output
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28 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
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29 ]]></command>
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30 <inputs>
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31 <conditional name="reference_source">
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32 <param name="reference_source_selector" type="select" label="Choose the source for the database">
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33 <option value="cached">Locally cached</option>
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34 <option value="history">History</option>
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35 </param>
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36 <when value="cached">
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37 <param name="database" type="select" label="Select database">
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38 <options from_data_table="all_fasta">
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39 <filter type="sort_by" column="2" />
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40 </options>
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41 <validator type="no_options" message="A built-in database is not available" />
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
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46 </when>
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47 </conditional>
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48 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
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49 <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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50 <option value="dna">dna - DNA sequence</option>
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51 <option value="prot">prot - protein sequence</option>
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52 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
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53 </param>
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54 <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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55 <option value="dna">dna - DNA sequence </option>
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56 <option value="rna">rna - RNA sequence</option>
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57 <option value="prot">prot - protein sequence</option>
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58 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
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59 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
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60 </param>
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61 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
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62 <option value="yes" selected="true">Yes, suppresses .psl header</option>
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63 <option value="no">No, do not suppresses .psl header</option>
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64 </param>
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65 <conditional name="mask_type">
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66 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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67 but may extend through it in nucleotide searches. Masked areas
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68 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
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69 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
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70 <option value="upper">upper - mask out upper-cased sequence</option>
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71 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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72 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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73 </param>
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74 <when value="lower" />
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75 <when value="upper" />
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76 <when value="out" />
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77 <when value="file.out">
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78 <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
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79 </when>
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80 </conditional>
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81 </inputs>
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82 <outputs>
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83 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
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84 </outputs>
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85 <tests>
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86 <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
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87 <test>
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88 <param name="reference_source_selector" value="history" />
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89 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
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90 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
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91 <param name="database_type" value="dnax" />
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92 <param name="query_type" value="rnax" />
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93 <param name="noHead" value="yes" />
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94 <param name="mask" value="lower" />
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95 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
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96 </test>
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97 <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
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98 <test>
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99 <param name="reference_source_selector" value="history" />
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100 <param name="database" value="dbia3/dbia3.fa" />
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101 <param name="query" value="dbia3/dmel-transcript.fa" />
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102 <param name="database_type" value="dnax" />
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103 <param name="query_type" value="rnax" />
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104 <param name="noHead" value="yes" />
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105 <param name="mask" value="lower" />
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106 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
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107 </test>
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108 <!-- test on the database masked by repeat masker -->
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109 <test>
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110 <param name="reference_source_selector" value="history" />
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111 <param name="database" value="dbia3/dbia3_masked.2bit" />
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112 <param name="query" value="dbia3/dmel-transcript.fa" />
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113 <param name="database_type" value="dnax" />
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114 <param name="query_type" value="rnax" />
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115 <param name="noHead" value="yes" />
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116 <param name="mask" value="file.out" />
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117 <param name="mask_file" value="dbia3/dbia3_RM.out" />
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118 <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" />
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119 </test>
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120
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121 </tests>
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122 <help>
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123 <![CDATA[
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124 BLAT
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125 ====
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126 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
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127
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128 blat (version: v340)- Standalone blat sequence search command line tool.
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129 -------------------------------------------------------------------------
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130
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131 usage:
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132 ++++++
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133
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134 $ blat database query [-ooc=11.ooc] output.psl
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135
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136 where:
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137 database and query are each either a .fa, .nib or .2bit file,
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138 or a list of these files with one file name per line.
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139 -ooc=11.ooc tells the program to load over-occurring 11-mers from
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140 an external file. This will increase the speed
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141 by a factor of 40 in many cases, but is not required.
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142 output.psl is the name of the output file.
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143
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144 documentation:
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145 ++++++++++++++
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146
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147 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
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148
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149 Source code:
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150 ++++++++++++
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151
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152 http://hgdownload.cse.ucsc.edu/admin/exe/
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153
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154 ]]></help>
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155 <citations>
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156 <citation type="doi">10.1101/gr.229202</citation>
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157 </citations>
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158 </tool>
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159
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160
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