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comparison siRNA.xml @ 0:07745c0958dd draft

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author big-tiandm
date Thu, 18 Sep 2014 21:40:25 -0400
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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 </requirements>
10
11 <command interpreter="perl">siRNA.pl
12 ## Change this to accommodate the number of threads you have available.
13 -t \${GALAXY_SLOTS:-4}
14
15 -path \$SCRIPT_PATH
16
17 #for $j, $s in enumerate( $series )
18 ##rank_of_series=$j
19 -i ${s.input}
20 -tag ${s.tag}
21 #end for
22
23 -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
24
25 ## Do or not annotate siRNAs by function
26 #if $params.function_anno == "yes":
27 -nat $params.nat -repeat $params.repeat
28 #end if
29
30 </command>
31
32 <inputs>
33
34 <repeat name="series" title="Series">
35 <param name="input" type="data" label="Raw data file"/>
36 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
37 </repeat>
38
39 <param name="format" type="select" lable="raw data format" multiple="false">
40 <option value="fastq">Raw data is fastq. format</option>
41 <option value="fasta">Raw data is fasta. format</option>
42 </param>
43
44 <param name="genome" type="data" label="genome sequence fasta file"/>
45 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
46 <param name="gff" type="data" label="gff file" />
47 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
48 <param name="rfam" type="data" label="rfam sequence file" />
49 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
50 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
51 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
52 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
53
54 <param name="p" type="select" lable="cluster method" multiple="false">
55 <option value="F">conventional</option>
56 <option value="T">NIBLES</option>
57 </param>
58 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
59
60
61 <conditional name="params">
62 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
63 <option value="no" selected="true">no</option>
64 <option value="yes">yes</option>
65 </param>
66 <when value="yes">
67 <param name="nat" type="data" label="atural antisense transcripts file" />
68 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
69 </when>
70 </conditional> <!-- params -->
71
72 <param name="cen" type="data" label="centromere file input" />
73 <param name="span" type="int" value="50000" label="plot span" />
74 <param name="deg" type="data" label="file config of de sample" />
75 </inputs>
76
77 <outputs>
78 <data format="txt" name="siRNA cluster" from_work_dir="./total.result"/>
79 <data format="txt" name="analysis result" from_work_dir="./result.html"/>
80
81 </outputs>
82
83 <help>
84
85 </help>
86 </tool>