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1 <tool id="plant_sirna_pipeline_v1" name="siRNA_pipeline" veision="1.0.0">
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2 <description>tool for plant siRNA analisis</description>
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3
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6 <requirement type="package" version="0.12.7">bowtie</requirement>
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7 <requirement type="package" version="3.0.1">R</requirement>
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8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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9 <requirement type="package" version="1.96">threads</requirement>
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10 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
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11 <requirement type="package" version="2.59">SVG</requirement>
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12 <requirement type="package" version="1.4_001">Boost-Graph</requirement>
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13 </requirements>
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14
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15 <command interpreter="perl">siRNA_pipeline.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
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19 -path \$SCRIPT_PATH
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20
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21 #for $j, $s in enumerate( $series )
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22 ##rank_of_series=$j
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23 -i ${s.input}
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24 -tag ${s.tag}
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25 #end for
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26
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27 ## prepare bowtie index
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28 #set index_path = ''
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29 #if str($reference_genome.source) == "history":
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30 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
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31 #set index_path = 'genome'
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32 #else:
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33 #set index_path = $reference_genome.index.fields.path
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34 #end if
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35
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36
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37 ## prepare Rfam bowtie index
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38 #set rfam_index_path = ''
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39 #if str($reference_rfam.source) == "history":
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40 bowtie-build "$reference_rfam.own_file" rfam; ln -s $reference_rfam.own_file" rfam.fa;
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41 #set rfam_index_path = 'rfam'
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42 #else:
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43 #set rfam_index_path = $reference_rfam.index.fields.path
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44 #end if
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45
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46
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47
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48 ## Do or not annotate siRNAs by function
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49 #if $params.function_anno == "yes":
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50 -nat $params.nat -repeat $params.repeat
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51 #end if
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52
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53 ## Do or not DEG
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54 #if $degseq.degseq_analysis == "yes" :
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55 -deg $degseq.deg
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56 #end if
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57
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58 -format $format -phred $phred -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v -a $a -n $mapnt -d $d -p $p -l $l -cen $cen -span $span > run.log
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59
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60 </command>
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61
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62 <inputs>
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63
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64 <repeat name="series" title="Series">
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65 <param name="input" type="data" label="Raw data file"/>
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66 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
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67 </repeat>
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68
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69 <param name="format" type="select" lable="raw data format" multiple="false">
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70 <option value="fastq">Raw data is fastq. format</option>
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71 <option value="fasta">Raw data is fasta. format</option>
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72 </param>
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73
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74 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
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75 <option value="64">Phred+64</option>
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76 <option value="33" selected="true">Phred+33</option>
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77 </param>
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78
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79 <conditional name="reference_genome">
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80 <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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81 <option value="indexed">Use a built-in index</option>
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82 <option value="history">Use one from the history</option>
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83 </param>
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84 <when value="indexed">
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85 <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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86 <options from_data_table="bowtie_indexes">
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87 <filter type="sort_by" column="2"/>
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88 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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89 </options>
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90 </param>
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91 </when>
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92 <when value="history">
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93 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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94 </when>
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95 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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96
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97 <conditional name="reference_rfam">
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98 <param name="source" type="select" label="Will you select a rfam reference 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 rfam 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="gff" type="data" label="gff file" />
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116 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
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117 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
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118 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
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119 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
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120 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
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121
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122 <param name="p" type="select" lable="cluster method" multiple="false">
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123 <option value="F">conventional</option>
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124 <option value="T">NIBLES</option>
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125 </param>
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126 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
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127
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128
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129 <conditional name="params">
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130 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
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131 <option value="no" selected="true">no</option>
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132 <option value="yes">yes</option>
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133 </param>
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134 <when value="yes">
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135 <param name="nat" type="data" label="atural antisense transcripts file" />
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136 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
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137 </when>
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138 </conditional> <!-- params -->
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139
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140 <param name="cen" type="data" label="centromere file input" />
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141 <param name="span" type="integer" value="50000" label="plot span" />
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142
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143 <conditional name="degseq">
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144 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
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145 <option value="no" selected="true">no</option>
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146 <option value="yes">yes</option>
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147 </param>
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148 <when value="yes">
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149 <param name="deg" type="data" label="file config of de sample" />
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150 </when>
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151 </conditional>
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152
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153 </inputs>
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154
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155 <outputs>
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156 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
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157 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
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158
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159 </outputs>
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160
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161 <help>
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162
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163 </help>
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164 </tool>
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