|
10
|
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>
|
|
|
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>
|
|
|
13 <requirement type="package" version="1.5.0">libx11</requirement>
|
|
|
14 </requirements>
|
|
|
15
|
|
|
16 <command interpreter="perl">siRNA.pl
|
|
|
17 ## Change this to accommodate the number of threads you have available.
|
|
|
18 -t \${GALAXY_SLOTS:-4}
|
|
|
19
|
|
|
20 -path \$SCRIPT_PATH
|
|
|
21
|
|
|
22 #for $j, $s in enumerate( $series )
|
|
|
23 ##rank_of_series=$j
|
|
|
24 -i ${s.input}
|
|
|
25 -tag ${s.tag}
|
|
|
26 #end for
|
|
|
27
|
|
|
28 ## Do or not annotate siRNAs by function
|
|
|
29 #if $params.function_anno == "yes":
|
|
|
30 -nat $params.nat -repeat $params.repeat
|
|
|
31 #end if
|
|
|
32
|
|
|
33 ## Do or not DEG
|
|
|
34 #if $degseq.degseq_analysis == "yes" :
|
|
|
35 -deg $degseq.deg
|
|
|
36 #end if
|
|
|
37
|
|
|
38 -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l -cen $cen -span $span > run.log
|
|
|
39
|
|
|
40 </command>
|
|
|
41
|
|
|
42 <inputs>
|
|
|
43
|
|
|
44 <repeat name="series" title="Series">
|
|
|
45 <param name="input" type="data" label="Raw data file"/>
|
|
|
46 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
|
|
|
47 </repeat>
|
|
|
48
|
|
|
49 <param name="format" type="select" lable="raw data format" multiple="false">
|
|
|
50 <option value="fastq">Raw data is fastq. format</option>
|
|
|
51 <option value="fasta">Raw data is fasta. format</option>
|
|
|
52 </param>
|
|
|
53
|
|
|
54 <param name="genome" type="data" label="genome sequence fasta file"/>
|
|
|
55 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
|
|
|
56 <param name="gff" type="data" label="gff file" />
|
|
|
57 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
|
|
|
58 <param name="rfam" type="data" label="rfam sequence file" />
|
|
|
59 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
|
|
|
60 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
|
|
|
61 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
|
|
|
62 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
|
|
|
63
|
|
|
64 <param name="p" type="select" lable="cluster method" multiple="false">
|
|
|
65 <option value="F">conventional</option>
|
|
|
66 <option value="T">NIBLES</option>
|
|
|
67 </param>
|
|
|
68 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
|
|
|
69
|
|
|
70
|
|
|
71 <conditional name="params">
|
|
|
72 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
|
|
|
73 <option value="no" selected="true">no</option>
|
|
|
74 <option value="yes">yes</option>
|
|
|
75 </param>
|
|
|
76 <when value="yes">
|
|
|
77 <param name="nat" type="data" label="atural antisense transcripts file" />
|
|
|
78 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
|
|
|
79 </when>
|
|
|
80 </conditional> <!-- params -->
|
|
|
81
|
|
|
82 <param name="cen" type="data" label="centromere file input" />
|
|
|
83 <param name="span" type="integer" value="50000" label="plot span" />
|
|
|
84
|
|
|
85 <conditional name="degseq">
|
|
|
86 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
|
|
|
87 <option value="no" selected="true">no</option>
|
|
|
88 <option value="yes">yes</option>
|
|
|
89 </param>
|
|
|
90 <when value="yes">
|
|
|
91 <param name="deg" type="data" label="file config of de sample" />
|
|
|
92 </when>
|
|
|
93 </conditional>
|
|
|
94
|
|
|
95 </inputs>
|
|
|
96
|
|
|
97 <outputs>
|
|
|
98 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
|
|
|
99 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
|
|
|
100
|
|
|
101 </outputs>
|
|
|
102
|
|
|
103 <help>
|
|
|
104
|
|
|
105 </help>
|
|
|
106 </tool>
|
