Mercurial > repos > bgruening > repeat_masker

annotate repeatmasker.xml @ 7:d7540a923c7b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 133126ca40437cebd8ead4ec14400dcc22b5ce21"
author iuc
date Sun, 01 Dec 2019 09:31:09 -0500
parents 65ab76d58c41
children ade773848c3d
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1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
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2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
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4 <requirements>
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5 <requirement type="package" version="4.0.7">repeatmasker</requirement>
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6 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 RM_PATH=\$(which RepeatMasker) &&
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10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
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11 RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
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12 mkdir lib &&
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13 export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
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14 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
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15 #if $repeat_source.source_type == "repbase":
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16 cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' &&
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17 #end if
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18 ln -s '${input_fasta}' rm_input.fasta &&
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19 RepeatMasker -dir \$(pwd)
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20 #if $repeat_source.source_type == "library":
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21 -lib '${repeat_source.repeat_lib}'
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22 -cutoff '${repeat_source.cutoff}'
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23 #else if $repeat_source.source_type == "repbase":
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24 #if $repeat_source.species_source.species_from_list == 'yes':
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25 $repeat_source.species_source.species_list
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26 #else
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27 -species '${repeat_source.species_source.species_name}'
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28 #end if
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29 #end if
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30 -parallel \${GALAXY_SLOTS:-1}
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31 ${gff}
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32 ${excln}
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33 ${advanced.is_only}
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34 ${advanced.is_clip}
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35 ${advanced.no_is}
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36 ${advanced.rodspec}
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37 ${advanced.primspec}
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38 ${advanced.nolow}
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39 ${advanced.noint}
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40 ${advanced.norna}
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41 ${advanced.alu}
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42 ${advanced.div}
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43 ${advanced.search_speed}
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44 -frag ${advanced.frag}
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45 ## -maxsize ${advanced.maxsize}
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46 #if str($advanced.gc):
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47 -gc ${advanced.gc}
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48 #end if
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49 ${advanced.gccalc}
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50 ${advanced.nocut}
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51 ${advanced.keep_alignments}
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52 ${advanced.invert_alignments}
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53 ${advanced.xout}
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54 ${advanced.xsmall}
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55 ${advanced.poly}
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56 rm_input.fasta &&
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57 #if $advanced.is_only != '-is_only':
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58 mv rm_input.fasta.masked '${output_masked_genome}' &&
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59 sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ; 1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
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60 mv rm_input.fasta.tbl '${output_table}' &&
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61 #if $gff == '-gff':
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62 mv rm_input.fasta.out.gff '${output_gff}' &&
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63 #end if
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64 #if $advanced.keep_alignments == '-ali':
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65 mv rm_input.fasta.align '${output_alignment}' &&
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66 #end if
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67 #if $advanced.poly == '-poly':
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68 sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
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69 #end if
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70 #end if
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71 if [ -f 'rm_input.fasta.cat.gz' ]; then
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72 zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
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73 else
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74 mv rm_input.fasta.cat '${output_repeat_catalog}';
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75 fi
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76 ]]>
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77 </command>
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78
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79 <inputs>
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80 <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />
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81 <conditional name="repeat_source">
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82 <param label="Repeat library source" name="source_type" type="select">
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83 <option selected="true" value="repbase">RepBase</option>
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84 <option value="library">Custom library of repeats</option>
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85 </param>
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86 <when value="repbase">
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87 <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />
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88 <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase -->
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89 <conditional name="species_source">
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90 <param label="Select species name from a list?" name="species_from_list" type="select">
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91 <option value="yes" selected="true">Yes</option>
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92 <option value="no">No</option>
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93 </param>
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94 <when value="yes">
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95 <param name="species_list" type="select" label="Species">
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96 <option value="-species anopheles" selected="true">anopheles</option>
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97 <option value="-species arabidopsis">arabidopsis</option>
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98 <option value="-species artiodactyl">artiodactyl</option>
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99 <option value="-species aspergillus">aspergillus</option>
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100 <option value="-species carnivore">carnivore</option>
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101 <option value="-species cat">cat</option>
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102 <option value="-species chicken">chicken</option>
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103 <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
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104 <option value="-species 'ciona savignyi'">ciona savignyi</option>
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105 <option value="-species cow">cow</option>
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106 <option value="-species danio">danio</option>
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107 <option value="-species diatoaea">diatomea</option>
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108 <option value="-species dog">dog</option>
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109 <option value="-species drosophila">drosophila</option>
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110 <option value="-species elegans">elegans</option>
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111 <option value="-species fugu">fugu</option>
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112 <option value="-species fungi" selected="true">fungi</option>
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113 <option value="-species human">human</option>
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114 <option value="-species maize">maize</option>
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115 <option value="-species mammal">mammal</option>
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116 <option value="-species mouse">mouse</option>
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117 <option value="-species pig">pig</option>
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118 <option value="-species rat">rat</option>
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119 <option value="-species rice">rice</option>
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120 <option value="-species rodentia">rodentia</option>
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121 <option value="-species ruminantia">ruminantia</option>
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122 <option value="-species wheat">wheat</option>
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123 </param>
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124 </when>
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125 <when value="no">
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126 <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" />
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127 </when>
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128 </conditional>
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129 </when>
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130 <when value="library">
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131 <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" />
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132 <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />
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133 </when>
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134 </conditional>
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135 <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" />
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136 <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" />
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137 <section name="advanced" title="Advanced options" expanded="false">
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138 <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" />
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139 <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" />
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140 <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" />
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141 <param argument="-rodspec" type="boolean" truevalue="-rodspec" falsevalue="" checked="false" label="Only check for rodent specific repeats" help="If this option is select a check for rodent specific repeats is done instead of a full RepeatMasker run" />
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142 <param argument="-primspec" type="boolean" truevalue="-primspec" falsevalue="" checked="false" label="Only check for primate specific repeats" help="If this option is select a check for primate specific repeats is done instead of a full RepeatMasker run" />
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143 <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="No low complexity masking" help="Skip masking of simple tandem repeats and low complexity regions." />
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144 <param argument="-noint" type="boolean" truevalue="-noint" falsevalue="" checked="false" label="No interspersed repeat masking" help="Only mask simple repeats, skip masking of interspersed repeats." />
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145 <param argument="-norna" type="boolean" truevalue="-norna" falsevalue="" checked="false" label="No repeat-like-RNA masking" help="Skip masking of small pol III transcribed RNA (these are masked by default because they resemble SINEs)" />
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146 <param argument="-alu" type="boolean" truevalue="-alu" falsevalue="" checked="false" label="Limit masking to (primate) Alu repeats" />
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147 <param argument="-div" type="boolean" truevalue="-div" falsevalue="" checked="false" label="Limit masking to less diverged (younger) repeats" />
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148 <param type="select" name="search_speed" label="Search speed vs sensitiviy trade-off">
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149 <option value="">Default</option>
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150 <option value="-q">Quick (5-10% less sensitive, 3-4 times speedup)</option>
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151 <option value="-qq">Rush (10% less sensitive)</option>
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152 <option value="-s">Slow (0-5% more sensitive, 2.5 times slowdown)</option>
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153 </param>
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154 <param type="integer" argument="-frag" value="40000" label="Maximum contiguous sequence searched" help="Maximum length of sequencing that is search without fragmenting" />
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155 <!-- -maxsize option is in the help, but not in the code of repeatmasker-->
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156 <!--param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" /-->
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157 <param type="integer" argument="-gc" optional="true" label="Select matrices for this GC%" help="Valid values are a percentage or -1 to choose the default" />
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158 <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" />
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159 <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" />
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160 <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" />
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161 <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" />
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162 <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" />
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163 <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Output repetitive regions as lowercase, non-repetitive regions as uppercase" />
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164 <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" />
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165 </section>
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166 </inputs>
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167 <outputs>
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168 <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}">
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169 <filter>not advanced['is_only']</filter>
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170 </data>
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171 <data name="output_log" format="tabular" label="RepeatMasker output log on ${on_string}">
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172 <filter>not advanced['is_only']</filter>
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173 </data>
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174 <data name="output_table" format="txt" label="RepeatMasker repeat statistics on ${on_string}">
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175 <filter>not advanced['is_only']</filter>
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176 </data>
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177 <data name="output_repeat_catalog" format="txt" label="RepeatMasker repeat catalogue on ${on_string}" />
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178 <data name="output_alignment" format="txt" label="RepeatMasker alignment on ${on_string}">
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179 <filter>not advanced['is_only'] and advanced['keep_alignments']</filter>
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180 </data>
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181 <data name="output_polymorphic" format="tabular" label="RepeatMasker possible polymorphic repeats on ${on_string}">
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182 <filter>not advanced['is_only'] and advanced['poly']</filter>
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183 </data>
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184 <data name="output_gff" format="gff" label="RepeatMasker repeat annotation on ${on_string}">
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185 <filter>not advanced['is_only'] and gff is True</filter>
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186 </data>
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187 </outputs>
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188 <tests>
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189 <test expect_num_outputs="4">
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190 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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191 <param name="source_type" value="library" />
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192 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
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193 <output name="output_masked_genome" file="small.fasta.masked" />
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194 <output name="output_table" file="small.fasta.stats" lines_diff="6" />
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195 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
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196 <output name="output_log" file="small.fasta.log" />
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197 </test>
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198 <test expect_num_outputs="7">
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199 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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200 <param name="source_type" value="library" />
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201 <param name="gff" value="-gff" />
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202 <!-- <param name="show" value="yes" /> -->
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203 <param name="keep_alignments" value="-ali" />
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204 <param name="poly" value="-poly" />
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205 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
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206 <output name="output_masked_genome" file="small.fasta.masked" />
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207 <output name="output_table" file="small.fasta.stats" lines_diff="6" />
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208 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
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209 <output name="output_log" file="small.fasta.log" />
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210 <output name="output_alignment" file="small.fasta.align" />
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211 <output name="output_polymorphic" file="small.fasta.poly" />
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212 <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
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213 </test>
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214 <test expect_num_outputs="4">
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215 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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216 <param name="source_type" value="repbase" />
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217 <param name="repbase_file" value="fake_repbase.embl" />
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218 <param name="repbase_file_name" value="fake.embl" />
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219 <param name="species_list" value="anopheles" />
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220 <output name="output_masked_genome" file="small.fasta.masked" />
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221 <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
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222 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
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223 <output name="output_log" file="small_repbase.fasta.log" />
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224 </test>
3
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225 </tests>
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226 <help><![CDATA[
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227 RepeatMasker is a program that screens DNA for interspersed repeats and low
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228 complexity DNA sequences. The database of repeats to screen for can be
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229 provided as a FASTA file or downloaded from RepBase_. If the RepBase option is
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230 chosen the RepBaseRepeatMaskerEdition file should be downloaded and
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231 unpacked, and the enclosed EMBL format file ('RMRBSeqs.embl') should
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232 be uploaded to Galaxy for use with this tool.
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233
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234 Further documentation is available on the RepeatMasker homepage_.
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235
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236 .. _RepBase: http://www.girinst.org/repbase/
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237 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
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238 ]]>
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239 </help>
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240 <citations>
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241 <citation type="bibtex">
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242 @misc{RepeatMasker,
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243 title = {RepeatMasker Open-4.0},
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244 howpublished = {\url{http://www.repeatmasker.org}},
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245 author = {Smit, AFA and Hubley, R and Green, P.},
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246 year = {2013-2015}}
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247 </citation>
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248 </citations>
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249 </tool>