Mercurial > repos > rnateam > graphclust_fasta_to_gspan

annotate fasta2shrep_gspan.xml @ 5:8641b7be8757 draft

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author rnateam
date Fri, 17 Mar 2017 08:28:05 -0400
parents aae41396646e
children fcb1bb6dc0f9
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1 <tool id="gspan" name="fasta_to_gspan" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.1.11">graphclust-wrappers</requirement>
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4 <requirement type="package" version="2.1.6">rnashapes</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
5
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11 fasta2shrep_gspan.pl
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12 --fasta '$dataFasta'
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13 $i_crop_unpaired_ends
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14 $i_abstr
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15 $i_stacks
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16 -t '3=0,5=80'
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17 -M $M
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18 -c $rel_energy_range
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19 -win $wins
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20 -shift $shift
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21 $u
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22 $seq_graph_t
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23 -group $group
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24
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param type="data" name="dataFasta" format="fasta" label="Input file in FASTA format" />
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29 <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean"
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30 label="Add stacking information to graphs." help="-stack"/>
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31 <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean"
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32 label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
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33 <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean"
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34 label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
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35 <param name="M" type="integer" value="5" label="Max number of shreps that should be taken per window." help="-M"/>
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36 <param name="rel_energy_range" type="integer" value="20"
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37 label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
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38 <param name="wins" type="text" value="40,150"
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39 label=" A list of window sizes to use" help="comma separated integers"/>
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40 <param name="shift" type="integer" value="30"
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41 label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
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42 <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean"
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43 label="Ignore unstable structures (RNAshapes)" help="-u"/>
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44 <param name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="True" type="boolean"
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45 label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
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46 <param name="group" type="integer" value="10000"
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47 label="Group size" help="by default 10000"/>
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48 </inputs>
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49 <outputs>
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50 <collection name="gspan_compressed" type="list" label="GSPAN Groups" >
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51 <discover_datasets pattern="(?P&lt;name&gt;.*)\.bz2$" directory="GSPAN_Outputs" />
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52 </collection>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="dataFasta" value="data.fasta"/>
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57 <param name="i_stacks" value="True" />
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58 <param name="i_abstr" value="False" />
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59 <param name="i_crop_unpaired_ends" value="False" />
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60 <param name="M" value="5" />
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61 <param name="rel_energy_range" value="20" />
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62 <param name="wins" value="40,150" />
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63 <param name="shift" value="30" />
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64 <param name="u" value="True" />
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65 <param name="seq_graph_t" value="True" />
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66 <param name="group" value="10000" />
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67 <output_collection name="gspan_compressed" type="list">
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68 <element name="1.group.gspan" file="GSPAN_Outputs/1.group.gspan.bz2"/>
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69 </output_collection>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
0
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74
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75 **What it does**
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76
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77 For each fragment of input sequence we use RNAshapes to create a set of structures.
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78 The default parameters for example consider for each input fragment again a
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79 window of size 40nt and 150nt with a window shift of 30%. This allows to
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80 consider local structures as well as global structures for a fragment.
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81 From each such RNAshape window we take the top 5 shreps (suboptimal
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82 structures for the top 5 shapes) within 20% of the mfe energy of that window
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83 and convert them into graphs.
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84 As shape level (abstraction level) we use 3 for short sequences and 5 for
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85 sequences >= 80nt. Please see also RNAshapes documentation for all these
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86 terms.
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87
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88
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89 **Parameters**
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90
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91 + **input** : Sequences in Fasta format.
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92
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93 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
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94 (type p) from each of the involved bases to the new vertex.
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95
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96 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
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97
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98 + **cue** : Crop unpaired ends. If you give this flag, then the unpaired ends of each single structure are ignored. E.g. the structure
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99 ...(((...))).. becomes just (((...)))
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100
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101 + **M** : Max number of shreps that should be taken per window.
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102
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103 + **c** : Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes) Use only one of -e and -c!
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104
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105 + **wins** : A list of window sizes to use. If none are given (empty string ''), then the entire sequence is taken with no windows. Each window > 1 required!
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106
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107 + **shift** : The shift of the window, relative to the window size given in percent. So you give which percent of the window size shall be
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108 used for the shift. Of course the shift is rounded down to the
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109 nearest whole number.
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110 Example 20 % of a window 150 would result in a step size of 30 nt.
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111 It is a relative parameter, as you can give different window sizes.
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112 If you do not give this parameter there is a default shift of 1 nt.
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113
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114 + **u** : Ignore unstable structures (RNAshapes). This option filters out closed structures with positive free energy.
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115
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116 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
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117
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118 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
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119
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120 ]]>
4
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121 </help>
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122 <citations>
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123 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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124 <citation type="doi">10.1093/bioinformatics/btu649</citation>
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125 </citations>
0
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126 </tool>