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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e
author rnateam
date Thu, 15 Nov 2018 01:15:35 -0500
parents 0554fa091710
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2
f9a7dc68d6cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e
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1 <tool id="rbc_rnacode" name="RNAcode" version="0.3.2">
0
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2 <description>Analyze the protein coding potential in MSA.</description>
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3 <requirements>
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4 <requirement type="package" version="0.3">rnacode</requirement>
2
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5 <requirement type="package" version="9.22">ghostscript</requirement>
0
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6 </requirements>
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7 <version_command>RNAcode --version</version_command>
1
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8 <command detect_errors="exit_code">
0
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9 <![CDATA[
1
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10 #if $cond_breakmaf.select_breakmaf == 'breakmaf'
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11 '$__tool_directory__/breakMAF.pl'
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12 --maxlength $cond_breakmaf.maxlength
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13 --desiredLength $cond_breakmaf.desiredlength
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14 < '$alignment' |
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15 #else
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16 cat '$alignment' |
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17 #end if
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19 #if $cond_breakmaf.select_breakmaf == 'breakmaf' and $cond_breakmaf.processseparately == 'yes'
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20 '$__tool_directory__/processMAF.sh'
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21 #else
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22 RNAcode
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23 #end if
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24
0
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25 $outputFormat
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26
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27 #if $cutoff and $cutoff is not None
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28 --cutoff $cutoff
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29 #end if
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30
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31 #if $num_samples and $num_samples is not None
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32 --num-samples $num_samples
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33 #end if
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34
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35 $stop_early
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36 $best_region
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37 $best_only
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38
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39 #if $cond_generateEPS.generateEPS == 'create'
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40 --eps
1
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41 --eps-dir eps/
0
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42 #if $cond_generateEPS.eps_cutoff and $cond_generateEPS.eps_cutoff is not None
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43 --eps-cutoff $cond_generateEPS.eps_cutoff
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44 #end if
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45 #end if
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46
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47 #if $cond_scoringParameters.scoringParameters == 'custom'
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48 --pars "$pars"
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49 #end if
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50
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51 #if $outputFormat.value == '--tabular'
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52 --outfile $outFileDefault
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53 #elif $outputFormat.value == '--gtf'
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54 --outfile $outFileGTF
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55 #end if
2
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56
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57 ## add missing header
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58 #if $cond_breakmaf.select_breakmaf != 'breakmaf' and $outputFormat.value == '--tabular':
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59 && sed -i -e "1 i\HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" $outFileDefault #end if
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60
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61 #if $cond_generateEPS.generateEPS == 'create'
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62 #if $cond_generateEPS.imgoutfmt == 'zipeps'
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63 && tar -czf '$out_eps_zip' eps
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64 #else if $cond_generateEPS.imgoutfmt == 'eps'
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65 && gs -sDEVICE=eps2write -dNOPAUSE -dBATCH -dSAFER -sOutputFile='$out_eps_mp' `ls -v eps/*.eps`
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66 #end if
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67 #end if
0
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68 ]]>
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69 </command>
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70 <inputs>
2
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71 <param name="alignment" type="data" format="maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/>
1
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72 <conditional name="cond_breakmaf">
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73 <param name="select_breakmaf" type="select" label="Break long alignment blocks" help="If your alignments contain blocks of long genomic regions it is usually not reasonable to score these long regions as a whole.">
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74 <option value="keepmaf" selected="true">Process original alignment</option>
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75 <option value="breakmaf">Break long alignment blocks</option>
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76 </param>
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77 <when value="breakmaf">
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78 <param argument="--maxLength" name="maxlength" type="integer" optional="true" value="400" label="maxLength" help="Break all blocks longer than that."/>
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79 <param argument="--desiredLength" name="desiredlength" type="integer" optional="true" value="200" label="desiredLength" help="Try to create blocks of this size."/>
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80 <param name="processseparately" type="boolean" value="false" truevalue="yes" falsevalue="no" label="process blocks separately" help="If enables RNAcode is called separately for each block. This might be a reasonable strategy if RNAcode fails for some blocks."/>
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81 </when>
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82 <when value="keepmaf"/>
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83 </conditional>
0
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84 <param argument="--cutoff" name="cutoff" type="float" optional="true" value="1.0" label="Cutoff" help="Show only regions that have a p-value below the given number. By default all hits are shown."/>
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85 <param argument="--num_samples" name="num_samples" type="integer" optional="true" value="100" label="Number of samples" help="Number of random alignments that are sampled to calculate the p-value. RNAcode estimates the significance of a coding prediction by sampling a given number of random alignments. Default is 100 which gives reasonably stable p-values that are useful for assessing the relevance of a prediction."/>
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86 <param argument="--stop_early" name="stop_early" type="boolean" truevalue="--stop-early" falsevalue="" checked="false" label="Stop early" help="Setting this option stops the sampling process as soon as it is clear that the best hit will not fall below the given p-value cutoff. For example, assume a p-value cutoff of 0.05 (see --cutoff) and a sample size of 1000 is given (see --num-samples). As soon as 50 random samples score better than the original alignment, the process is stopped and all hits in the original alignment are reported as p>0.05 (or by convention as 1.0 in gtf and tabular output)."/>
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87 <param argument="--best_region" name="best_region" type="boolean" truevalue="--best-region" falsevalue="" checked="false" label="Show only best non-overlapping hits" help="By default all positive scoring segments are shown in the output if they fall below the given p-value cutoff. If two hits overlap (different frame or different strand) and --best_region is given only the hit with the highest score is shown. Strong coding regions often lead to statistically significant signals also in other frames. These hits are suppressed by this option and only the correct reading frame is reported."/>
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88 <param argument="--best_only" name="best_only" type="boolean" truevalue="--best-only" falsevalue="" checked="false" label="Show only best hit" help="This options shows only the one single best hit for each alignment."/>
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89 <conditional name="cond_scoringParameters">
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90 <param name="scoringParameters" type="select" label="Scoring parameters" help="">
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91 <option value="default" selected="true">Default</option>
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92 <option value="custom">Custom</option>
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93 </param>
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94 <when value="default"/>
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95 <when value="custom">
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96 <param argument="--pars" name="pars" type="text" label="Scoring parameters as comma separated string:'DELTA,OMEGA,omega,stop_penalty'" help="See the appendix of the Paper for an explanation for the meaning of these parameters. Default: '-10.0,-4.0,-2.0,-8.0'"/>
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97 </when>
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98 </conditional>
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99 <conditional name="cond_generateEPS">
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100 <param name="generateEPS" type="select" label="Create plots" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)">
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101 <option value="create">Create Plots</option>
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102 <option value="nocreate" selected="true">Do not generate EPS plots</option>
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103 </param>
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104 <when value="create">
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105 <param argument="--eps_cutoff" name="eps_cutoff" type="float" optional="true" value="0.05" label="Create plots only for high scoring segments with p better than:" help=""/>
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106 <param name="imgoutfmt" type="select" label="Output format" help="For larger numbers of high scoring segments output to a collection can be slow. Choose zipped or single page eps in this case.">
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107 <option value="sepeps" selected="true">separate eps in collection</option>
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108 <option value="zipeps">zipped eps</option>
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109 <option value="eps">multi page eps</option>
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110 </param>
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111 </when>
0
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112 <when value="nocreate"/>
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113 </conditional>
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114
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115 <param name="outputFormat" type="select" label="Output format">
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116 <option value="--tabular" selected="true">Default</option>
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117 <option value="--gtf">GTF genome annotation file</option>
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118 </param>
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119 </inputs>
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120 <outputs>
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121 <data name="outFileDefault" format="tabular" label="${tool.name} on ${on_string}">
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122 <filter>outputFormat == '--tabular'</filter>
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123 </data>
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124 <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}">
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125 <filter>outputFormat == '--gtf'</filter>
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126 </data>
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127 <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string} (plots)">
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128 <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "sepeps"</filter>
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129 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps"/>
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130 </collection>
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131 <data name="out_eps_zip" format="zip" label="${tool.name} on ${on_string} (plots)">
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132 <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "zipeps"</filter>
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133 </data>
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134 <data name="out_eps_mp" format="eps" label="${tool.name} on ${on_string} (plots)">
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135 <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "eps"</filter>
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136 </data>
0
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137 </outputs>
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138 <tests>
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139 <test>
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140 <param name="alignment" value="coding.aln"/>
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141 <param name="outputFormat" value="--tabular"/>
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142 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
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143 <conditional name="cond_generateEPS">
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144 <param name="generateEPS" value="create"/>
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145 <param name="eps_cutoff" value="0.05"/>
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146 <param name="imgoutfmt" value="sepeps" />
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147 </conditional>
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148 <output_collection name="output_eps" type="list" count="2">
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149 <element name="hss-0" file="hss-0.eps" ftype="eps" compare="sim_size" delta="50000"/>
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150 <element name="hss-1" file="hss-1.eps" ftype="eps" compare="sim_size" delta="50000"/>
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151 </output_collection>
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152 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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153 </test>
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154 <test>
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155 <param name="alignment" value="coding.aln"/>
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156 <conditional name="cond_generateEPS">
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157 <param name="generateEPS" value="create"/>
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158 <param name="eps_cutoff" value="0.05"/>
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159 <param name="imgoutfmt" value="zipeps" />
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160 </conditional>
1
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161 <param name="outputFormat" value="--tabular"/>
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162 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
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163 <output name="out_eps_zip" ftype="zip" file="eps.tar.gz" compare="sim_size" delta="50000"/>
1
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164 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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165 </test>
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166 <test>
0
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167 <param name="alignment" value="coding.maf"/>
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168 <conditional name="cond_breakmaf">
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169 <param name="select_breakmaf" value="breakmaf"/>
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170 </conditional>
2
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171 <conditional name="cond_generateEPS">
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172 <param name="generateEPS" value="create"/>
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173 <param name="eps_cutoff" value="0.05"/>
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174 <param name="imgoutfmt" value="eps" />
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175 </conditional>
1
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176 <param name="outputFormat" value="--gtf"/>
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177 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
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178 <output name="out_eps_mp" ftype="eps" file="eps.eps" compare="sim_size" delta="50000"/>
1
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179 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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180 </test>
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181 <test>
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182 <param name="alignment" value="coding.maf"/>
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183 <conditional name="cond_breakmaf">
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184 <param name="select_breakmaf" value="breakmaf"/>
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185 <param name="processseparately" value="yes"/>
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186 </conditional>
0
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187 <param name="generateEPS" value="nocreate"/>
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188 <param name="outputFormat" value="--gtf"/>
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189 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
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190 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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191 </test>
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192 </tests>
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193 <help>
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194 <![CDATA[
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195 **RNAcode**
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196 Predicts protein coding regions in an alignment of homologous
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197 nucleotide sequences. The prediction is based on evolutionary
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198 signatures typical for protein genese, i.e. the presence of
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199 synonyomous/conservative nucleotide mutations, conservation of the
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200 reading frame and absence of stop codons.
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201
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202 RNAcode does not rely on any species specific sequence characteristics
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203 whatsoever and does not use any machine learning techniques. The only
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204 input required for RNAcode is a multiple sequence alignment either in
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205 MAF or Clustal W format. RNAcode reports local regions of unusual high
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206 coding potential together with an associated p-value.
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207
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208 **Input alignment**
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209
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210 The input alignment needs to be formatted in ClustalW format or MAF
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211 format (http://genome.ucsc.edu/FAQ/FAQformat#format5). The latter
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212 format allows to include genomic coordinates which can be used to
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213 produce annotation files.
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214
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215 Important: RNAcode uses the first sequence as reference sequence,
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216 i.e. all results and reported coding regions apply to this reference
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217 sequence.
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218
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219 Currently the alignments has to contain at least 3 sequences. Gaps
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220 have to be given as dash ('-'). Unspecified letters given as 'N' are
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221 allowed and treated neutrally during all calculations. No difference is
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222 made between uppercase or lowercase input, i.e. 'softly'-repeat masked
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223 sequences which use lowercase letters for masked regions are treated
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224 the same way as unmasked sequences.
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225
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226 **Output format**
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227
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228 In the default output each prediction is reported on one line by 10 fields.
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229
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230 1. HSS id
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231 Unique running number for each high scoring segment
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232 predicted in one RNAcode call
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233
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234 2. Frame
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235 The reading frame phasing relative to the starting
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236 nucleotide position in the reference sequence. +1 means
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237 that the first nucleotide in the reference sequence is in
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238 the same frame as the predicted coding region. Negative
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239 frames indicate that the predicted regions are on the
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240 reverse complement strand.
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241
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242 3. Length
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243 The length of the predicted region in amino acids
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244
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245 4. From 5. To
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246 The position of the first/last amino acid in the translated
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247 nucleotide sequence of the reference sequence starting
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248 with 1.
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249
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250 6. Name
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251 The name of the reference sequence as given in the input alignment.
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252
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253 7. Start 8. End
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254 The nucleotide position in the reference sequence of the
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255 predicted coding region. If no genomic coordinates are given
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256 (if you provide a CLUSTAL W as input) the first nucleotide position in
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257 the references sequence is set to 1, otherwise the positions are the
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258 1-based genomic coordinates as given in the input MAF file.
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259
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260 9. Score
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261 The coding potential score. High scores indicate high coding potential.
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262
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263 10. P
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264 The p-value associated with the score. This is the probability
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265 that a random alignment with same properties contains an equally good
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266 or better hit.
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267 ]]>
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268 </help>
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269 <citations>
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270 <citation type="doi">10.1261/rna.2536111</citation>
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271 </citations>
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272 </tool>