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1 <tool id="plant_sirna_v1" name="siRNA" 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="2.11.0">R</requirement>
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8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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3
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9 <requirement type="perl-module">threads</requirement>
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10 <requirement type="perl-module">Parallel-ForkManager</requirement>
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11 <requirement type="perl-module">SVG</requirement>
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12 <requirement type="perl-module">Boost-Graph</requirement>
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13 </requirements>
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14
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15 <command interpreter="perl">siRNA.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 -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l -deg $deg -cen $cen -span $span
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28
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29 ## Do or not annotate siRNAs by function
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30 #if $params.function_anno == "yes":
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31 -nat $params.nat -repeat $params.repeat
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32 #end if
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33
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34 </command>
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35
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36 <inputs>
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37
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38 <repeat name="series" title="Series">
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39 <param name="input" type="data" label="Raw data file"/>
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40 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
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41 </repeat>
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42
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43 <param name="format" type="select" lable="raw data format" multiple="false">
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44 <option value="fastq">Raw data is fastq. format</option>
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45 <option value="fasta">Raw data is fasta. format</option>
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46 </param>
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47
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48 <param name="genome" type="data" label="genome sequence fasta file"/>
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49 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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50 <param name="gff" type="data" label="gff file" />
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51 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
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52 <param name="rfam" type="data" label="rfam sequence file" />
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53 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
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54 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
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55 <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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56 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
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57
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58 <param name="p" type="select" lable="cluster method" multiple="false">
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59 <option value="F">conventional</option>
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60 <option value="T">NIBLES</option>
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61 </param>
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62 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
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63
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64
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65 <conditional name="params">
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66 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
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67 <option value="no" selected="true">no</option>
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68 <option value="yes">yes</option>
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69 </param>
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70 <when value="yes">
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71 <param name="nat" type="data" label="atural antisense transcripts file" />
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72 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
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73 </when>
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74 </conditional> <!-- params -->
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75
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76 <param name="cen" type="data" label="centromere file input" />
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77 <param name="span" type="integer" value="50000" label="plot span" />
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78 <param name="deg" type="data" label="file config of de sample" />
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79 </inputs>
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80
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81 <outputs>
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82 <data format="txt" name="siRNA cluster" from_work_dir="./total.result"/>
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83 <data format="txt" name="analysis result" from_work_dir="./result.html"/>
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84
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85 </outputs>
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86
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87 <help>
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88
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89 </help>
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90 </tool>
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