Mercurial > repos > bgruening > rnaz_window

annotate rnazWindow.xml @ 0:2436fa5c7d53 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 03:57:47 -0500
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1 <tool id="rnaz_window" name="RNAz windows" version="2.1">
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2 <requirements>
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3 <requirement type="package" version="2.1">rnaz</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 rnazWindow.pl
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7 --window $window
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8 --slide $slide
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9 --max-length $maxlength
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10 --max-gap $maxgap
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11 --max-masked $maxmask
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12 --min-id $minid
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13 --min-seqs $minseqs
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14 --max-seqs $maxseqs
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15 --num-samples $numsamples
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16 --min-length $minlength
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17 --opt-id $optid
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18 --$forward_or_reverse
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19 #if $noref:
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20 $noref
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21 #end ifx
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22 '$input'
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23 > '$output'
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24 ]]></command>
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25 <inputs>
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26 <param format="txt" name="input" type="data" label="Input Alignment File" />
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27 <param argument="--window" name="window" type="integer" value="120" min="80" label="Window size, default 120" />
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28 <param argument="--slide" name="slide" type="integer" value="120" min="1" label="Window step size, default 120" />
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29 <param argument="--max-length" name="maxlength" type="integer" value="120" label="Min size of block before slicing, default is window size 120" />
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30 <param argument="--max-gap" name="maxgap" type="float" value="0.25" label="Maximum fraction of gaps, default 0.25" />
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31 <param argument="--max-masked" name="maxmask" type="float" value="0.1" label="Maximum fraction of masked letters in sequence, default 0.1" />
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32 <param argument="--min-id" name="minid" type="integer" value="50"
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33 label="Discard alignment windows with an overall mean pairwise identity smaller than X%. (Default: 50)" />
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34 <param argument="--min-seqs" name="minseqs" type="integer" value="2"
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35 label="Minimum number of sequences in an alignment. Discard any windows with less than N sequences (Default:2)" />
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36 <param argument="--max-seqs" name="maxseqs" type="integer" value="6"
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37 label="Maximum number of sequences in an alignment. Discard any windows with less than N sequences (Default:6)" />
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38 <param argument="--num-samples" name="numsamples" type="integer" value="1"
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39 label="Number of different subsets of sequences that is sampled if there are more sequences in the alignment than --max-seqs (Default: 1)" />
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40 <param argument="--min-length" name="minlength" type="integer" value="0"
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41 label="Minimum number of columns of an alignment slice. After removing sequences from the alignment, all-gap columns are removed. If the resulting alignment has fewer than N columns, the complete alignment is discarded." />
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42 <param argument="--opt-id" name="optid" type="integer" value="80"
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43 label="If the number of sequences has to be reduced (see --max-seqs) a subset of sequences is chosen which is optimized for this value of mean pairwise identity. (In percent, default: 80)" />
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44 <param name="forward_or_reverse" type="select" label="Scored strand">
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45 <option value="forward">Score forward strand (-f)</option>
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46 <option value="reverse">Score reverse strand (-r)</option>
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47 <option value="both-strands" selected="true">Score both strands (-b)</option>
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48 </param>
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49 <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
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50 label="By default the first sequence is interpreted as reference sequence. This means, for example, that if the reference sequence is removed during filtering steps the complete alignment is discarded. Also, if there are too many sequences in the alignment, the reference sequence is never removed when choosing an appropriate subset. Having a reference sequence is crucial if you are doing screens of genomic regions. For some other applications it might not be necessary and in such cases you can change the default behaviour by setting this option." />
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51 </inputs>
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52
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53 <outputs>
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54 <data name="output" format="txt" />
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input" value="unknown.aln"/>
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60 <output name="output" file="unknown.aln.window"/>
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61 </test>
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62 <test>
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63 <param name="input" value="tRNA.maf"/>
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64 <output name="output" file="tRNA.maf.window"/>
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65 </test>
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66 </tests>
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67
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68 <help>
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69 <![CDATA[
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70
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71 RNAz cannot score alignments longer than 400
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72 columns. In practice, it is generally advisable that you score
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73 long alignments, say more than 200 columns, in shorter, overlapping
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74 windows. For general purpose screens we recommend a window
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75 size of 120. This window size appears large enough to detect
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76 local secondary structures within long ncRNAs and, on the
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77 other hand, small enough to find short secondary structures
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78 without loosing the signal in a much too long window
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79
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80 Usage: rnazWindow.pl [options] [file]
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81 Options:
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82 -w, --window=N Size of the window (Default: 120)
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83
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84 -s, --slide=N Step size (Default: 120)
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85
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86 -m, --max-length Slice only alignments longer than N columns. This
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87 means blocks longer than the window size given by --window but shorter
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88 than N are kept intact and not sliced. Per default this length is set
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89 to the window size given by --window (or 120 by default).
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90
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91 --max-gap=X Maximum fraction of gaps. If a reference sequence is used
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92 (i.e. "--no-reference" is not set), each sequence is compared to the
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93 reference sequence and if in the pairwise comparison the fraction of
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94 columns with gaps is higher than X the sequence is discarded. If no
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95 reference sequence is used, all sequences with a fraction of gaps
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96 higher than X are discarded. (Default: 0.25)
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97
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98 --max-masked=X Maximum fraction of masked (=lowercase letters) in a
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99 sequence. All sequences with a fraction of more than X lowercase
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100 letters are discarded. This is usually used for excluding repeat
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101 sequences marked by RepeatMasker but any other information can be
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102 encoded by using lowercase letters. (Default: 0.1)
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103
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104 --min-id=X Discard alignment windows with an overall mean pairwise
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105 identity smaller than X%. (Default: 50)
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106
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107 --min-seqs=N Minimum number of sequences in an alignment. Discard any
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108 windows with less than N sequences (Default:2).
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109
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110 --max-seqs=N Maximum number of sequences in an alignment. If the
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111 number of sequences in a window is higher than N, a subset of
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112 sequences is used with exactly N sequences. The greedy algorithm of
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113 the program "rnazSelectSeqs.pl" is used which optimizes for a user
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114 specified mean pairwise identity (see "--opt-id"). (Default: 6)
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115
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116 --num-samples=N Number of different subsets of sequences that is
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117 sampled if there are more sequences in the alignment than
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118 "--max-seqs". (Default: 1)
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119
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120 --min-length=N Minimum number of columns of an alignment slice. After
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121 removing sequences from the alignment, all-gap columns are
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122 removed. If the resulting alignment has fewer than N columns, the
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123 complete alignment is discarded.
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124
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125 --opt-id=X If the number of sequences has to be reduced (see
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126 "--max-seqs") a subset of sequences is chosen which is optimized for
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127 this value of mean pairwise identity. (In percent, default: 80)
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128
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129 --max-id=X One sequence from pairs with pairwise identity higher than
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130 X % this is removed (default: 99, i.e. only almost identical sequences
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131 are removed) NOT IMPLEMENTED
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132
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133 --forward --reverse --both-strands Output forward, reverse complement
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134 or both of the sequences in the windows. Please note: "RNAz" has the
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135 same options, so if you use "rnazWindow.pl" for an RNAz screen, we
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136 recommend to set the option directly in "RNAz" and leave the default
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137 here. (Default: ---forward)
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138
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139 --no-reference By default the first sequence is interpreted as
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140 reference sequence. This means, for example, that if the reference
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141 sequence is removed during filtering steps the complete alignment is
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142 discarded. Also, if there are too many sequences in the alignment, the
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143 reference sequence is never removed when choosing an appropriate
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144 subset. Having a reference sequence is crucial if you are doing
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145 screens of genomic regions. For some other applications it might not
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146 be necessary and in such cases you can change the default behaviour by
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147 setting this option.
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148
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149 ]]>
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150 </help>
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151 <citations>
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152 <citation type="doi">10.1142/9789814295291_0009</citation>
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153 </citations>
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154 </tool>