|
0
|
1 <tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
|
|
|
2 <description>tool for plant siRNA analisis</description>
|
|
|
3
|
|
|
4 <requirements>
|
|
|
5 <requirement type="set_environment">SCRIPT_PATH</requirement>
|
|
|
6 <requirement type="package" version="0.12.7">bowtie</requirement>
|
|
|
7 <requirement type="package" version="2.11.0">R</requirement>
|
|
|
8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
|
|
4
|
9 <requirement type="package" version="1.96">threads</requirement>
|
|
|
10 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
|
|
|
11 <requirement type="package" version="2.59">SVG</requirement>
|
|
|
12 <requirement type="package" version="1.4">Boost-Graph</requirement>
|
|
0
|
13 </requirements>
|
|
|
14
|
|
|
15 <command interpreter="perl">siRNA.pl
|
|
|
16 ## Change this to accommodate the number of threads you have available.
|
|
|
17 -t \${GALAXY_SLOTS:-4}
|
|
|
18
|
|
|
19 -path \$SCRIPT_PATH
|
|
|
20
|
|
|
21 #for $j, $s in enumerate( $series )
|
|
|
22 ##rank_of_series=$j
|
|
|
23 -i ${s.input}
|
|
|
24 -tag ${s.tag}
|
|
|
25 #end for
|
|
|
26
|
|
|
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
|
|
|
28
|
|
|
29 ## Do or not annotate siRNAs by function
|
|
|
30 #if $params.function_anno == "yes":
|
|
|
31 -nat $params.nat -repeat $params.repeat
|
|
|
32 #end if
|
|
|
33
|
|
|
34 </command>
|
|
|
35
|
|
|
36 <inputs>
|
|
|
37
|
|
|
38 <repeat name="series" title="Series">
|
|
|
39 <param name="input" type="data" label="Raw data file"/>
|
|
|
40 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
|
|
|
41 </repeat>
|
|
|
42
|
|
|
43 <param name="format" type="select" lable="raw data format" multiple="false">
|
|
|
44 <option value="fastq">Raw data is fastq. format</option>
|
|
|
45 <option value="fasta">Raw data is fasta. format</option>
|
|
|
46 </param>
|
|
|
47
|
|
|
48 <param name="genome" type="data" label="genome sequence fasta file"/>
|
|
|
49 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
|
|
|
50 <param name="gff" type="data" label="gff file" />
|
|
|
51 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
|
|
|
52 <param name="rfam" type="data" label="rfam sequence file" />
|
|
|
53 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
|
|
|
54 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
|
|
|
55 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
|
|
|
56 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
|
|
|
57
|
|
|
58 <param name="p" type="select" lable="cluster method" multiple="false">
|
|
|
59 <option value="F">conventional</option>
|
|
|
60 <option value="T">NIBLES</option>
|
|
|
61 </param>
|
|
|
62 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
|
|
|
63
|
|
|
64
|
|
|
65 <conditional name="params">
|
|
|
66 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
|
|
|
67 <option value="no" selected="true">no</option>
|
|
|
68 <option value="yes">yes</option>
|
|
|
69 </param>
|
|
|
70 <when value="yes">
|
|
|
71 <param name="nat" type="data" label="atural antisense transcripts file" />
|
|
|
72 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
|
|
|
73 </when>
|
|
|
74 </conditional> <!-- params -->
|
|
|
75
|
|
|
76 <param name="cen" type="data" label="centromere file input" />
|
|
1
|
77 <param name="span" type="integer" value="50000" label="plot span" />
|
|
0
|
78 <param name="deg" type="data" label="file config of de sample" />
|
|
|
79 </inputs>
|
|
|
80
|
|
|
81 <outputs>
|
|
|
82 <data format="txt" name="siRNA cluster" from_work_dir="./total.result"/>
|
|
|
83 <data format="txt" name="analysis result" from_work_dir="./result.html"/>
|
|
|
84
|
|
|
85 </outputs>
|
|
|
86
|
|
|
87 <help>
|
|
|
88
|
|
|
89 </help>
|
|
|
90 </tool>
|
