Mercurial > repos > rnateam > locarna_reliability_profile

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:52:31 +0000
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1 <tool id="locarna_reliability_profile" name="LocARNA reliability-profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>
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3 Plot reliability profile for probabilistic mlocarna
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version" />
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12
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13 <command><![CDATA[
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14 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
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15 then tar xzf '$input_archive' ;
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16 else tar xf '$input_archive' ;
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17 fi)
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18 &&
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19 reliability-profile.pl mlocarna_results
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20
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21 --output-format='$output_format'
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22
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23 #if $output_format == 'pdf'
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24 --out '$pdf_output_plot'
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25 #else if $output_format == 'png'
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26 --out '$png_output_plot'
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27 #end if
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28
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29 #if str($title) != ""
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30 --title '$title'
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31 #end if
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33 #if str($seqname) != ""
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34 --seqname '$seqname'
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35 #end if
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37 --beta $beta
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38 --structure-weight $structure_weight
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39
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40 #if str($signals)!=""
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41 --signals '$signals'
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42 #end if
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44 --offset $offset
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45
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46 #if $write_rscript:
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47 --write-R-script '$rscript_output'
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48 #end if
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49
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50 #if $write_subsequence
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51 --write-subseq
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52 #end if
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53
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54 $predict
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55 $fit_once_on
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56 $show_sw
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57 $rev_compl
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58
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59 > '$stdout'
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60 ]]></command>
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61
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62 <inputs>
4
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63 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive" help="Archive of MLocARNA results (tar or tar.gz as generated by running mlocarna in probabilistic alignment mode)."/>
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64 <param name="title" type="text" label="Plot title" help="Title of the plot"/>
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65 <param name="seqname" type="text" label="Reference sequence" help="Project to a reference sequence. Provide one of the sequence names in the alignment input or leave blank to plot without projection."/>
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66 <param argument="--dont-predict" name="predict" type="boolean" checked="true" truevalue="" falsevalue="--dont-predict" help="Turn on/off predicting."/>
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67 <param argument="--fit-once-on" type="boolean" checked="false" truevalue="--fit-once-on" falsevalue="" help="Predict exactly one 'on'-region"/>
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68 <param argument="--show-sw" type="boolean" checked="true" truevalue="--show-sw" falsevalue="" help="Show the influence of structure weight."/>
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69 <param argument="--revcompl" name="rev_compl" type="boolean" checked="false" truevalue="--revcompl" falsevalue="" help="Plot and fit a reverse complement."/>
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70 <param argument="--beta" help="Inverse temperature for fitting." type="float" value="12.0" min="1.0" max="25.0"/>
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71 <param argument="--structure-weight" type="float" value="1.0" min="0.0" max="8.0" help="Weight of structure against sequence (1.0 means equal)"/>
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72 <param argument="--offset" help="Genomic offset." type="integer" value="1"/>
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73 <param argument="--signals" type="text" label="List of signals" help="List of '{from to} orientation' signal specifications. Show signals in plot and compared infered signal to them. Ranges 'from to' can be repeated; the orientation must be either +1 or -1.The specifications of the single signals are separated by ';'. Example of two signal,where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1">
0
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74 <sanitizer invalid_char=" ">
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75 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
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76 </sanitizer>
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77 </param>
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78
4
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79 <param name="output_format" type="select" label="Output options">
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80 <option value="pdf" selected="true">Plot in pdf format</option>
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81 <option value="png" selected="false">Plot in png format</option>
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82 </param>
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83
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84 <param name="write_rscript" type="boolean" argument="--write-R-script" label="Write R script" checked="false" help="Write R script that can produce the output plot."/>
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85 <param name="write_subsequence" type="boolean" argument="--write-subseq" label="Write Subsequence" checked="false" help="Write subsequence in output."/>
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86 </inputs>
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87
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88
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89 <outputs>
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90 <data format="pdf" name="pdf_output_plot" label="${tool.name} on ${on_string}: PDF plot">
0
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91 <filter>output_format == 'pdf'</filter>
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92 </data>
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93 <data format="png" name="png_output_plot" label="${tool.name} on ${on_string}: PNG plot">
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94 <filter>output_format == 'png'</filter>
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95 </data>
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96 <data format="txt" name="rscript_output" label="${tool.name} on ${on_string}: R script ">
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97 <filter> write_rscript is True </filter>
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98 </data>
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99 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
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100 </outputs>
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101
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102 <tests>
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103 <test expect_num_outputs="3">
0
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104 <param name="input_archive" value="archaea.tar.gz" />
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105 <param name="write_rscript" value="true" />
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106 <output name="pdf_output_plot">
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107 <assert_contents>
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108 <has_text text="%PDF"/>
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109 <has_size value="5401" delta="100"/>
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110 </assert_contents>
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111 </output>
0
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112 <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
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113 <output name="stdout">
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114 <assert_contents>
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115 <has_text text="ONOFF"/>
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116 <has_text text="FIT"/>
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117 </assert_contents>
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118 </output>
0
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119 </test>
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120 </tests>
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121
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122 <help><![CDATA[**Reliability Profiles for Multiple RNA
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123 Alignment**
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124
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125 This tool draws reliability profiles for mlocarna alignments that have
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126 been computed in probabilistic alignment mode. Moreover, it predicts
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127 reliably aligned regions, which can be used to determine the
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128 boundaries of well conserved structured RNA motifs in less closely
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129 related sequence context.
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130
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131 **Input.**
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132 Results archive of an alignment by the mlocarna tool; for this
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133 purpose, mlocarna must be run in probabilistic mode in order to
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134 generate the required reliability information.
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135
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136 **Output.**
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137 Plot of the reliability profile for the input alignment. Moreover,
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138 a signal prediction is performed and predicted regions are
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139 annotated in the plot.
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140
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141
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142 For more information, see
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143 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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144 ]]></help>
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145
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146 <expand macro="citations" />
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147
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148 </tool>