Mercurial > repos > big-tiandm > sirna_plant

comparison siRNA.xml @ 21:9dcffd531c76 draft

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author big-tiandm
date Wed, 05 Nov 2014 21:09:35 -0500
parents 22d79320085c
children 206f92933924
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20:2ed1e1728299 21:9dcffd531c76
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="3.0.1">R</requirement>
8 <requirement type="package" version="1.20.0">degseq</requirement>
9 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
10 <requirement type="package" version="1.96">threads</requirement>
11 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
12 <requirement type="package" version="2.59">SVG</requirement>
13 <requirement type="package" version="1.4">Boost-Graph</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>