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1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0">
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2 <description>
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3 <![CDATA[
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4 identification of novel and known miRNAs
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5 ]]>
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6 </description>
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7 <requirements>
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8 <requirement type="package" version="2.0">mirdeep2</requirement>
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9 <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
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10 <requirement type="package" version="0.12.7">bowtie</requirement>
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11 <requirement type="package" version="5.18.1">perl</requirement>
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12 <requirement type="package" version="1.8.5">vienna_rna</requirement>
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13 <requirement type="package" version="2.023">pdf_api2</requirement>
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14 <requirement type="package" version="2.0">randfold</requirement>
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15 </requirements>
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16
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17 <command>
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18 <![CDATA[
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19 miRDeep2.pl
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20
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21 $reads
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22 $genome
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23 $mappings
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24
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25 #if $mature_this
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26 $mature_this
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27 #else
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28 none
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29 #end if
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30
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31 #if $mature_other
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32 $mature_other
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33 #else
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34 none
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35 #end if
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36
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37 #if $precursors
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38 $precursors
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39 #else
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40 none
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41 #end if
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42
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43 #if $species.value != 'all'
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44 -t $species
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45 #end if
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46
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47 #if $star_sequences
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48 -s $star_sequences
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49 #end if
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50
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51 #if $min_read_stack
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52 -a $min_read_stack
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53 #end if
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54
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55 #if $min_read_stack
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56 -a $min_read_stack
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57 #end if
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58
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59 -g $max_precursors_analyze
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60 -b $min_score_cutoff
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61 $disable_randfold
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62
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63 ; cp result*.bed result.bed 2> /dev/null
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64 ; cp result*.csv result.csv 2> /dev/null
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65 ; cp mirdeep_runs/run*/output.mrd . 2> /dev/null
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66 ; cp mirdeep_runs/run*/survey.csv . 2> /dev/null
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67
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68 ## html output
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69 ;
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70 cp result*.html $html 2> /dev/null
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71
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72 ## move pdf directory to be accessible from the new index.html
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73 ;
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74 mkdir -p $html.files_path 2> /dev/null
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75 ;
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76 cp -R pdfs* $html.files_path 2> /dev/null
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77
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78 ]]>
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79 </command>
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80 <stdio>
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81 <!-- Anything other than zero is an error -->
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82 <exit_code range="1:" />
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83 <exit_code range=":-1" />
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84 <!-- In case the return code has not been set propery check stderr too -->
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85 <regex match="Error:" />
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86 <regex match="Exception:" />
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87 </stdio>
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88 <inputs>
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89 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads">
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90 <help>
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91 <![CDATA[
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92 Reads in fasta format. The identifier should contain a prefix, a running
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93 number and a '_x' to indicate the number of reads that have this sequence.
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94 There should be no redundancy in the sequences.
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95 ]]>
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96 </help>
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97 </param>
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98 <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/>
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99 <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/>
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100 <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species"
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101 help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/>
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102 <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species">
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103 <help>
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104 <![CDATA[
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105 miRBase miRNA sequences in fasta format. These should be the pooled known
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106 mature sequences for 1-5 species closely related to the species being analyzed.
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107 ]]>
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108 </help>
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109 </param>
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110 <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences"
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111 help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/>
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112
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113 <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)">
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114 <option value="all">All species</option>
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115 <option value="tni">tetraodon</option>
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116 <option value="dps">d.pseudoobscura</option>
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117 <option value="dya">d.yakuba</option>
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118 <option value="ame">a.mellifera</option>
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119 <option value="dmo">d.mojavensis</option>
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120 <option value="cel">worm</option>
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121 <option value="aga">a.gambiae</option>
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122 <option value="cbr">c.briggsae</option>
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123 <option value="cin">c.intestinalis</option>
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124 <option value="mmu">mouse</option>
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125 <option value="xtr">x.tropicalis</option>
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126 <option value="eca">horse</option>
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127 <option value="cfa">dog</option>
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128 <option value="fru">fugu</option>
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129 <option value="bta">cow</option>
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130 <option value="der">d.erecta</option>
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131 <option value="dgr">d.grimshawi</option>
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132 <option value="gga">chicken</option>
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133 <option value="spu">s.purpuratus</option>
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134 <option value="bfl">lancelet</option>
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135 <option value="ptr">chimp</option>
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136 <option value="dse">d.sechellia</option>
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137 <option value="dpe">d.persimilis</option>
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138 <option value="dvi">d.virilis</option>
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139 <option value="rno">rat</option>
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140 <option value="dme">d.melanogaster</option>
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141 <option value="lca">cat</option>
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142 <option value="sja">c.japonica</option>
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143 <option value="dan">d.ananassae</option>
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144 <option value="hsa">human</option>
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145 <option value="dsi">d.simulans</option>
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146 </param>
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147 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
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148
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149 <param name="min_read_stack" optional="true" type="integer" minvalue="0" label="Minimum read stack height">
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150 <help>
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151 <![CDATA[
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152 minimum read stack height that triggers analysis. Using this option disables
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153 automatic estimation of the optimal value and all detected precursors are analyzed. (-a)
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154 ]]>
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155 </help>
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156 </param>
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157 <param name="max_precursors_analyze" type="integer" value="50000" label="Maximum precursors"
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158 help="Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g)."/>
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159 <param name="min_score_cutoff" type="integer" value="0" label="Minimum miRNA score"
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160 help="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)"/>
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161 <param name="disable_randfold" type="boolean" truevalue="-c" falsevalue="" label="Disable randfold analysis" help="(-c)"/>
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162 </inputs>
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163 <outputs>
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164 <data name="tab_results" format="tabular" from_work_dir="result.csv" label="Tabular output of ${tool.name} on ${on_string}"/>
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165 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
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166 <data name="pred_acc" format="tabular" from_work_dir="survey.csv" label="Prediction accuracy output of ${tool.name} on ${on_string}"/>
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167 <data name="bed_out" format="bed" from_work_dir="result.bed" label="Bed output of ${tool.name} on ${on_string}"/>
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168 <data name="mrd_out" format="txt" from_work_dir="output.mrd" label="Text output of ${tool.name} on ${on_string}"/>
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169 </outputs>
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170 <tests>
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171 <test>
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172 <param name="reads" value="reads_collapsed.fa"/>
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173 <param name="genome" value="cel_cluster.fa"/>
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174 <param name="mappings" value="reads_collapsed_vs_genome.arf"/>
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175 <param name="mature_this" value="mature_ref_this_species.fa"/>
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176 <param name="mature_other" value="mature_ref_other_species.fa"/>
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177 <param name="precursors" value="precursors_ref_this_species.fa"/>
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178
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179 <output name="tab_results" file="result.csv" compare="sim_size"/>
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180 <output name="prec_acc" file="survey.csv" compare="sim_size"/>
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181 <output name="bed_out" file="result.bed" compare="sim_size"/>
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182 <output name="mrd_out" file="output.mrd" compare="sim_size"/>
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183 </test>
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184 </tests>
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185 <help>
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186 <![CDATA[
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187 **What MiRDeep2 does**
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188
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189 MiRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.
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190 ]]>
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191 </help>
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192 <citations>
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193 <citation type="doi">10.1093/nar/gkr688</citation>
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194 <citation type="doi">10.1002/0471250953.bi1210s36</citation>
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195 </citations>
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196 </tool>
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