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1 <tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0">
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2 <description>tool for plant microRNA analisis</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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6 <requirement type="package" version="0.12.7">bowtie</requirement>
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7 <requirement type="set_environment">SCRIPT_PATH</requirement>
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8 <!--requirement type="package" version="3.0.1">R</requirement!-->
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9 <requirement type="package" version="2.59">SVG</requirement>
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10 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
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11 </requirements>
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12
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13 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
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14
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15 <command interpreter="perl">miRPlant.pl
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16 ## Change this to accommodate the number of threads you have available.
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17 -t \${GALAXY_SLOTS:-4}
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18 -path \$SCRIPT_PATH
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19
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20 #for $j, $s in enumerate( $series )
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21 ##rank_of_series=$j
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22 -i ${s.input}
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23 -tag ${s.tag}
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24 #end for
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25
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50
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26 ## prepare bowtie index
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27 #set index_path = ''
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28 #if str($reference_genome.source) == "history":
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29 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
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30 #set index_path = 'genome'
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31 #else:
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32 #set index_path = $reference_genome.index.fields.path
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33 #end if
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34
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35
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36 ## Do or not annotate rfam non-miRNA RNAs
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37 #if $params.annotate_rfam == "yes":
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38
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39 ## prepare Rfam bowtie index
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40 #set rfam_index_path = ''
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41 #if str($params.annotate_rfam.reference_rfam.source) == "history":
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42 bowtie-build "$params.annotate_rfam.reference_rfam.own_file" rfam; ln -s "$params.annotate_rfam.reference_rfam.own_file" rfam.fa;
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43 #set rfam_index_path = 'rfam'
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44 #else:
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45 #set rfam_index_path = $params.annotate_rfam.reference_rfam.index.fields.path
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46 #end if
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47
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48 -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v
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49 ## Do or not delet rfam mapped tags
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50 #if $params.annotate_rfam.rfamresult.delet_rfam == "yes":
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51 -D
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52 #end if
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53 #end if
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54
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55
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56 ## Do or not annotate known microRNAs
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57 #if $params.known_microRNA == "yes":
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58 -pre $pre -mat $mat
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59 #end if
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60
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61
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62 -format $format -gfa ${index_path}.fa -idx $index_path -phred $phred -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
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49
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63 </command>
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64
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65 <inputs>
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66
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67 <repeat name="series" title="Series">
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68 <param name="input" type="data" label="Raw data"/>
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69 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
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70 </repeat>
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71
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50
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72 <conditional name="reference_genome">
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73 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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74 <option value="indexed">Use a built-in index</option>
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75 <option value="history">Use one from the history</option>
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76 </param>
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77 <when value="indexed">
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78 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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79 <options from_data_table="bowtie_indexes">
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80 <filter type="sort_by" column="2"/>
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81 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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82 </options>
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83 </param>
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84 </when>
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85 <when value="history">
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86 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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87 </when>
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88 </conditional>
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89
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90 <conditional name="params">
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91 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
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92 <option value="yes" selected="true">yes</option>
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93 <option value="no">no</option>
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94 </param>
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95 <when value="yes">
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96 <!--param name="rfam" type="data" label="rfam sequence file" /-->
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97 <conditional name="reference_rfam">
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98 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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99 <option value="indexed">Use a built-in index</option>
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100 <option value="history">Use one from the history</option>
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101 </param>
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102 <when value="indexed">
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103 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
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104 <options from_data_table="rfam_bowtie_indexes">
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105 <filter type="sort_by" column="2"/>
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106 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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107 </options>
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108 </param>
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109 </when>
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110 <when value="history">
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111 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
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112 </when>
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113 </conditional>
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114
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115 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
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116
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117 <conditional name="rfamresult">
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118 <param name="delet_rfam" type="select" label="delet rfam mapped reads">
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119 <option value="yes" selected="true">yes</option>
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120 <option value="no">no</option>
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121 </param>
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122 </conditional> <!-- params -->
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123
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124
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125 </when>
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126 </conditional> <!-- params -->
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127
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128
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49
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129 <!--param name="input" format="tabular" type="data" label="input config file" /-->
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130
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131 <param name="format" type="select" lable="raw data format" multiple="false">
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132 <option value="fastq">Raw data is fastq. format</option>
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133 <option value="fasta">Raw data is fasta. format</option>
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134 </param>
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50
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135
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136 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
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137 <option value="64">Phred+64</option>
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138 <option value="33" selected="true">Phred+33</option>
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139 </param>
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140
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141 <conditional name="reference_genome">
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142 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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143 <option value="indexed">Use a built-in index</option>
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144 <option value="history">Use one from the history</option>
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145 </param>
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146 <when value="indexed">
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147 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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148 <options from_data_table="bowtie_indexes">
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149 <filter type="sort_by" column="2"/>
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150 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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151 </options>
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152 </param>
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153 </when>
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154 <when value="history">
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155 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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156 </when>
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157 </conditional>
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158
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159 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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160 <conditional name="params">
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161 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
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162 <option value="yes" selected="true">yes</option>
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163 <option value="no">no</option>
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164 </param>
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165 <when value="yes">
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166 <param name="mat" type="data" label="mature microRNA sequence file" />
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167 <param name="pre" type="data" label="precursor microRNA sequence fie" />
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168 </when>
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169 </conditional> <!-- params -->
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170
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171 <conditional name="params">
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172 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
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173 <option value="yes" selected="true">yes</option>
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174 <option value="no">no</option>
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175 </param>
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176 <when value="yes">
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177 <!--param name="rfam" type="data" label="rfam sequence file" /-->
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178 <when value="yes">
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179 <!--param name="rfam" type="data" label="rfam sequence file" /-->
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180 <conditional name="reference_rfam">
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181 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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182 <option value="indexed">Use a built-in index</option>
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183 <option value="history">Use one from the history</option>
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184 </param>
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185 <when value="indexed">
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186 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
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187 <options from_data_table="rfam_bowtie_indexes">
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188 <filter type="sort_by" column="2"/>
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189 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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190 </options>
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191 </param>
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192 </when>
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193 <when value="history">
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194 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
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195 </when>
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196 </conditional>
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197
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198 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
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199 </when>
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200 </conditional> <!-- params -->
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201
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202 <!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
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203 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
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204 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
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205 <param name="min" type="integer" value="19" label="minimum microRNA length" />
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206 <param name="max" type="integer" value="28" label="maximum microRNA length" />
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207 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
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208 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
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209 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
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210 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
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211 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
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212 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
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213 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
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214 </inputs>
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215
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216 <outputs>
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217 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
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218 <filter>(params['known_microRNA'] == 'Yes')</filter>
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219 </data>
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220 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
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221 <filter>(params['known_microRNA'] == 'Yes')</filter>
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222 </data>
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223 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
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224 <filter>(params['known_microRNA'] == 'Yes')</filter>
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225 </data>
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226 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
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227 <filter>(params['known_microRNA'] == 'Yes')</filter>
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228 </data>
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229 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
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230 <filter>(params['known_microRNA'] == 'Yes')</filter>
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231 </data>
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232 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
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233 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
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234 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
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235 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
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236 </outputs>
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237
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238 <help>
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239
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240 </help>
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241 </tool>
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