Mercurial > repos > rnateam > locarna_reliability_profile

annotate locarna_reliability_profile.xml @ 3:e84d1fc87829 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 14:29:00 +0000
parents 9942e1b7646c
children 7d63908343c3
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e84d1fc87829 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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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
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10 <expand macro="requirements" />
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11
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12 <expand macro="stdio" />
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13
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14 <expand macro="version" />
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16 <command><![CDATA[
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17 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
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18 then tar xzf '$input_archive' ;
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19 else tar xf '$input_archive' ;
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20 fi)
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21 &&
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22 reliability-profile.pl mlocarna_results
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23
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24 --output-format='$output_format'
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25
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26 #if $output_format == 'pdf'
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27 --out '$pdf_output_plot'
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28 #else if $output_format == 'png'
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29 --out '$png_output_plot'
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30 #end if
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31
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32 #if str($title) != ""
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33 --title '$title'
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34 #end if
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36 #if str($seqname) != ""
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37 --seqname '$seqname'
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38 #end if
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39
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40 --beta $beta
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41 --structure-weight $structure_weight
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42
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43 #if str($signals)!=""
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44 --signals '$signals'
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45 #end if
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46
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47 --offset $offset
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48
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49 #if $write_rscript:
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50 --write-R-script '$rscript_output'
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51 #end if
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52
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53 #if $write_subsequence
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54 --write-subseq
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55 #end if
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56
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57 $predict
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58 $fit_once_on
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59 $show_sw
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60 $rev_compl
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61
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62 > '$stdout'
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63 ]]></command>
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64
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65 <inputs>
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66 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive"
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67 help="Archive of MLocARNA results (tar or tar.gz as generated by running
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68 mlocarna in probabilistic alignment mode)." />
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69
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70 <param name="title" type="text" label="Plot title"
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71 help="Title of the plot"
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72 />
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73
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74 <param name="seqname" type="text" label="Reference sequence"
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75 help="Project to a reference sequence. Provide one of the sequence names in the alignment input
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76 or leave blank to plot without projection."
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77 />
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78
3
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79 <param argument="--dont-predict" name="predict" type="boolean" checked="true"
0
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80 truevalue="" falsevalue="--dont-predict"
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81 help="Turn on/off predicting."
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82 />
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83
3
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84 <param argument="--fit-once-on" type="boolean" checked="false"
0
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85 truevalue="--fit-once-on" falsevalue=""
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86 help="Predict exactly one 'on'-region"
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87 />
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88
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89 <param argument="--show-sw" type="boolean" checked="true"
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90 truevalue="--show-sw" falsevalue=""
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91 help="Show the influence of structure weight."
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92 />
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93
3
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94 <param argument="--revcompl" name="rev_compl" type="boolean" checked="false"
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95 truevalue="--revcompl" falsevalue=""
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96 help="Plot and fit a reverse complement."
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97 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98
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99 <param argument="--beta" help="Inverse temperature for fitting."
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100 type="float" value="12.0" min="1.0" max="25.0" />
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101
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102 <param argument="--structure-weight"
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103 type="float" value="1.0" min="0.0" max="8.0"
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104 help="Weight of structure against sequence (1.0 means equal)"
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105 />
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106
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107 <param argument="--offset" help="Genomic offset."
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108 type="integer" value="1" />
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109
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110 <param argument="--signals" type="text" label="List of signals"
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111 help="List of '{from to} orientation' signal specifications. Show signals in plot
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112 and compared infered signal to them. Ranges 'from to' can be repeated;
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113 the orientation must be either +1 or -1.
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114 The specifications of the single signals are separated by ';'. Example of two signal,
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115 where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1"
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116 >
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117 <sanitizer invalid_char=" ">
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118 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
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119 </sanitizer>
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120 </param>
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121
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122 <param name="output_format" type="select"
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123 label="Output options">
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124 <option value="pdf" selected="true">Plot in pdf
0
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125 format</option>
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126 <option value="png" selected="false">Plot in png format</option>
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127 </param>
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128
3
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129 <param name="write_rscript" type="boolean" argument="--write-R-script"
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130 label="Write R script" checked="false"
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131 help="Write R script that can produce the output plot."
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132 />
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133
3
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134 <param name="write_subsequence" type="boolean" argument="--write-subseq"
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135 label="Write Subsequence" checked="false"
0
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136 help="Write subsequence in output."
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137 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138
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139 </inputs>
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140
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141
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142 <outputs>
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143 <data format="pdf" name="pdf_output_plot"
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144 label="${tool.name} on ${on_string}: plot">
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145 <filter>output_format == 'pdf'</filter>
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146 </data>
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147 <data format="png" name="png_output_plot"
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148 label="${tool.name} on ${on_string}: plot">
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149 <filter>output_format == 'png'</filter>
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150 </data>
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151 <data format="txt" name="rscript_output"
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152 label="${tool.name} on ${on_string}: R script ">
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153 <filter> write_rscript is True </filter>
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154 </data>
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155 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
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156 </outputs>
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157
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158 <tests>
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159 <test expect_num_outputs="3">
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160 <param name="input_archive" value="archaea.tar.gz" />
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161 <param name="write_rscript" value="true" />
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162 <output name="pdf_output_plot">
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163 <assert_contents>
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164 <has_text text="%PDF"/>
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165 <has_size value="5401" delta="100"/>
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166 </assert_contents>
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167 </output>
0
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168 <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
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169 <output name="stdout">
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170 <assert_contents>
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171 <has_text text="ONOFF"/>
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172 <has_text text="FIT"/>
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173 </assert_contents>
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174 </output>
0
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175 </test>
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176 </tests>
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177
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178 <help><![CDATA[**Reliability Profiles for Multiple RNA
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179 Alignment**
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180
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181 This tool draws reliability profiles for mlocarna alignments that have
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182 been computed in probabilistic alignment mode. Moreover, it predicts
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183 reliably aligned regions, which can be used to determine the
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184 boundaries of well conserved structured RNA motifs in less closely
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185 related sequence context.
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186
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187 **Input.**
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188 Results archive of an alignment by the mlocarna tool; for this
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189 purpose, mlocarna must be run in probabilistic mode in order to
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190 generate the required reliability information.
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191
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192 **Output.**
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193 Plot of the reliability profile for the input alignment. Moreover,
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194 a signal prediction is performed and predicted regions are
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195 annotated in the plot.
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196
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197
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198 For more information, see
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199 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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200 ]]></help>
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201
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202 <expand macro="citations" />
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203
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204 </tool>