Mercurial > repos > bgruening > repeat_masker

annotate repeatmasker.xml @ 3:bdfc22c1c3e3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
author iuc
date Wed, 02 May 2018 20:18:11 -0400
parents
children 04f5c3d7448e
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3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
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1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7" profile="17.01">
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2 <description>RepeatMasker</description>
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3
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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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7
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8 <command detect_errors="exit_code"><![CDATA[
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9 RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries &&
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10 mkdir lib &&
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11 export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
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12 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
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13 #if $repeat_source.source_type == "repbase":
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14 cp '${repeat_source.repbase_file}' lib/RMRBSeqs.embl &&
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15 #end if
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16 ln -s '${input_fasta}' rm_input.fasta &&
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17 RepeatMasker -dir \$(pwd)
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18 #if $repeat_source.source_type == "library":
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19 -lib '${repeat_source.repeat_lib}'
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20 -cutoff '${repeat_source.cutoff}'
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21 #else if $repeat_source.source_type == "repbase":
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22 #if $repeat_source.species_source.species_from_list == 'yes':
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23 $repeat_source.species_source.species_list
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24 #else
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25 -species '${repeat_source.species_source.species_name}'
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26 #end if
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27 #end if
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28 -parallel \${GALAXY_SLOTS:-1}
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29 '${gff}'
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30 '${ignore_n_stretches}'
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31 '${advanced.is_only}'
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32 '${advanced.is_clip}'
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33 '${advanced.no_is}'
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34 '${advanced.rodspec}'
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35 '${advanced.primspec}'
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36 '${advanced.nolow}'
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37 '${advanced.noint}'
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38 '${advanced.norna}'
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39 '${advanced.alu}'
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40 '${advanced.div}'
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41 '${advanced.search_speed}'
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42 '${advanced.frag}'
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43 '${advanced.maxsize}'
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44 #if $advanced.gc is not None:
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45 '${advanced.gc}'
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46 #end if
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47 '${advanced.gccalc}'
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48 '${advanced.nocut}'
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49 '${advanced.keep_alignments}'
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50 '${advanced.invert_alignments}'
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51 '${advanced.xout}'
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52 '${advanced.xsmall}'
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53 '${advanced.poly}'
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54 rm_input.fasta &&
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55 #if $advanced.is_only != '-is_only':
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56 mv rm_input.fasta.masked '${output_masked_genome}' &&
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57 sed -r '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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58 mv rm_input.fasta.tbl '${output_table}' &&
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59 #if $gff == '-gff':
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60 mv rm_input.fasta.out.gff '${output_gff}' &&
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61 #end if
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62 #if $advanced.keep_alignments == '-ali':
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63 mv rm_input.fasta.align '${output_alignment}' &&
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64 #end if
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65 #if $advanced.poly == '-poly':
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66 sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
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67 #end if
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68 #end if
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69 mv rm_input.fasta.cat '${output_repeat_catalog}'
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70 ]]>
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71 </command>
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72
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73 <inputs>
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74 <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />
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75 <conditional name="repeat_source">
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76 <param label="Repeat library source" name="source_type" type="select">
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77 <option selected="true" value="repbase">RepBase</option>
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78 <option value="library">Custom library of repeats</option>
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79 </param>
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80 <when value="repbase">
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81 <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />
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82 <conditional name="species_source">
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83 <param label="Select species name from a list?" name="species_from_list" type="select">
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84 <option value="yes" selected="true">Yes</option>
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85 <option value="no">No</option>
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86 </param>
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87 <when value="yes">
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88 <param name="species_list" type="select" label="Species">
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89 <option value="-species anopheles" selected="true">anopheles</option>
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90 <option value="-species arabidopsis">arabidopsis</option>
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91 <option value="-species artiodactyl">artiodactyl</option>
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92 <option value="-species aspergillus">aspergillus</option>
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93 <option value="-species carnivore">carnivore</option>
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94 <option value="-species cat">cat</option>
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95 <option value="-species chicken">chicken</option>
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96 <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
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97 <option value="-species 'ciona savignyi'">ciona savignyi</option>
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98 <option value="-species cow">cow</option>
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99 <option value="-species danio">danio</option>
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100 <option value="-species diatoaea">diatomea</option>
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101 <option value="-species dog">dog</option>
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102 <option value="-species drosophila">drosophila</option>
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103 <option value="-species elegans">elegans</option>
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104 <option value="-species fugu">fugu</option>
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105 <option value="-species fungi" selected="true">fungi</option>
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106 <option value="-species human">human</option>
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107 <option value="-species maize">maize</option>
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108 <option value="-species mammal">mammal</option>
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109 <option value="-species mouse">mouse</option>
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110 <option value="-species pig">pig</option>
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111 <option value="-species rat">rat</option>
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112 <option value="-species rice">rice</option>
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113 <option value="-species rodentia">rodentia</option>
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114 <option value="-species ruminantia">ruminantia</option>
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115 <option value="-species wheat">wheat</option>
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116 </param>
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117 </when>
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118 <when value="no">
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119 <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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120 </when>
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121 </conditional>
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122 </when>
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123 <when value="library">
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124 <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" />
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125 <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />
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126 </when>
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127 </conditional>
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128 <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" />
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129 <param name="ignore_n_stretches" type="boolean" argument="-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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130 <section name="advanced" title="Advanced options" expanded="false">
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131 <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" />
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132 <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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133 <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" />
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134 <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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135 <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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136 <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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137 <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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138 <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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139 <param argument="-alu" type="boolean" truevalue="-alu" falsevalue="" checked="false" label="Limit masking to (primate) Alu repeats" />
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140 <param argument="-div" type="boolean" truevalue="-div" falsevalue="" checked="false" label="Limit masking to less diverged (younger) repeats" />
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141 <param type="select" name="search_speed" label="Search speed vs sensitiviy trade-off">
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142 <option value="">Default</option>
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143 <option value="-q">Quick (5-10% less sensitive, 3-4 times speedup)</option>
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144 <option value="-qq">Rush (10% less sensitive)</option>
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145 <option value="-s">Slow (0-5% more sensitive, 2.5 times slowdown)</option>
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146 </param>
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147 <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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148 <param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" />
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149 <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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150 <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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151 <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" />
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152 <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" />
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153 <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" />
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154 <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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155 <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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156 <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" />
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157 </section>
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158 </inputs>
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159 <outputs>
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160 <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}">
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161 <filter>not advanced['is_only']</filter>
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162 </data>
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163 <data name="output_log" format="tabular" label="RepeatMasker output log on ${on_string}">
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164 <filter>not advanced['is_only']</filter>
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165 </data>
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166 <data name="output_table" format="txt" label="RepeatMasker repeat statistics on ${on_string}">
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167 <filter>not advanced['is_only']</filter>
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168 </data>
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169 <data name="output_repeat_catalog" format="txt" label="RepeatMasker repeat catalogue on ${on_string}" />
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170 <data name="output_alignment" format="txt" label="RepeatMasker alignment on ${on_string}">
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171 <filter>not advanced['is_only'] and advanced['keep_alignments']</filter>
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172 </data>
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173 <data name="output_polymorphic" format="tabular" label="RepeatMasker possible polymorphic repeats on ${on_string}">
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174 <filter>not advanced['is_only'] and advanced['poly']</filter>
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175 </data>
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176 <data name="output_gff" format="gff" label="RepeatMasker repeat annotation on ${on_string}">
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177 <filter>not advanced['is_only'] and gff is True</filter>
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178 </data>
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179 </outputs>
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180 <tests>
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181 <test expect_num_outputs="4">
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182 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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183 <param name="source_type" value="library" />
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184 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
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185 <output name="output_masked_genome" file="small.fasta.masked" />
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186 <output name="output_table" file="small.fasta.stats" lines_diff="2" />
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187 <output name="output_repeat_catalog" file="small.fasta.cat" />
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188 <output name="output_log" file="small.fasta.log" />
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189 </test>
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190 <test expect_num_outputs="7">
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191 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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192 <param name="source_type" value="library" />
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193 <param name="gff" value="-gff" />
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194 <!-- <param name="show" value="yes" /> -->
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195 <param name="keep_alignments" value="-ali" />
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196 <param name="poly" value="-poly" />
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197 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
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198 <output name="output_masked_genome" file="small.fasta.masked" />
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199 <output name="output_table" file="small.fasta.stats" lines_diff="4" />
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200 <output name="output_repeat_catalog" file="small.fasta.cat" />
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201 <output name="output_log" file="small.fasta.log" />
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202 <output name="output_alignment" file="small.fasta.align" />
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203 <output name="output_polymorphic" file="small.fasta.poly" />
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204 <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
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205 </test>
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206 </tests>
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207 <help><![CDATA[
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208 RepeatMasker is a program that screens DNA for interspersed repeats and low
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209 complexity DNA sequences. The database of repeats to screen for can be
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210 provided as a FASTA file or downloaded from RepBase_. If the RepBase option is
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211 chosen the RepBaseRepeatMaskerEdition file should be downloaded and
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212 unpacked, and the enclosed EMBL format file ('RMRBSeqs.embl') should
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213 be uploaded to Galaxy for use with this tool.
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214
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215 Further documentation is available on the RepeatMasker homepage_.
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216
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217 .. _RepBase: http://www.girinst.org/repbase/
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218 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
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219 ]]>
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220 </help>
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221 <citations>
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222 <citation type="bibtex">
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223 @misc{RepeatMasker,
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224 title = {RepeatMasker Open-4.0},
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225 howpublished = {\url{http://www.repeatmasker.org}},
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226 author = {Smit, AFA and Hubley, R and Green, P.},
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227 year = {2013-2015}}
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228 </citation>
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229 </citations>
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230 </tool>