annotate siRNA.xml @ 28:e93f33f03019 draft

Uploaded
author big-tiandm
date Thu, 13 Nov 2014 22:45:51 -0500
parents 22d79320085c
children 206f92933924
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
1 <tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
2 <description>tool for plant siRNA analisis</description>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
3
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
4 <requirements>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
5 <requirement type="set_environment">SCRIPT_PATH</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
6 <requirement type="package" version="0.12.7">bowtie</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
7 <requirement type="package" version="3.0.1">R</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
8 <requirement type="package" version="1.20.0">degseq</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
9 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
10 <requirement type="package" version="1.96">threads</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
11 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
12 <requirement type="package" version="2.59">SVG</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
13 <requirement type="package" version="1.4">Boost-Graph</requirement>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
14 </requirements>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
15
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
16 <command interpreter="perl">siRNA.pl
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
17 ## Change this to accommodate the number of threads you have available.
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
18 -t \${GALAXY_SLOTS:-4}
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
19
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
20 -path \$SCRIPT_PATH
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
21
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
22 #for $j, $s in enumerate( $series )
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
23 ##rank_of_series=$j
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
24 -i ${s.input}
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
25 -tag ${s.tag}
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
26 #end for
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
27
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
28 ## Do or not annotate siRNAs by function
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
29 #if $params.function_anno == "yes":
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
30 -nat $params.nat -repeat $params.repeat
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
31 #end if
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
32
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
33 ## Do or not DEG
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
34 #if $degseq.degseq_analysis == "yes" :
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
35 -deg $degseq.deg
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
36 #end if
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
37
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
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
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
39
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
40 </command>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
41
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
42 <inputs>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
43
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
44 <repeat name="series" title="Series">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
45 <param name="input" type="data" label="Raw data file"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
46 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
47 </repeat>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
48
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
49 <param name="format" type="select" lable="raw data format" multiple="false">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
50 <option value="fastq">Raw data is fastq. format</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
51 <option value="fasta">Raw data is fasta. format</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
52 </param>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
53
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
54 <param name="genome" type="data" label="genome sequence fasta file"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
55 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
56 <param name="gff" type="data" label="gff file" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
57 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
58 <param name="rfam" type="data" label="rfam sequence file" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
59 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
60 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
61 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
62 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
63
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
64 <param name="p" type="select" lable="cluster method" multiple="false">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
65 <option value="F">conventional</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
66 <option value="T">NIBLES</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
67 </param>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
68 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
69
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
70
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
71 <conditional name="params">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
72 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
73 <option value="no" selected="true">no</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
74 <option value="yes">yes</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
75 </param>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
76 <when value="yes">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
77 <param name="nat" type="data" label="atural antisense transcripts file" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
78 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
79 </when>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
80 </conditional> <!-- params -->
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
81
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
82 <param name="cen" type="data" label="centromere file input" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
83 <param name="span" type="integer" value="50000" label="plot span" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
84
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
85 <conditional name="degseq">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
86 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
87 <option value="no" selected="true">no</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
88 <option value="yes">yes</option>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
89 </param>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
90 <when value="yes">
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
91 <param name="deg" type="data" label="file config of de sample" />
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
92 </when>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
93 </conditional>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
94
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
95 </inputs>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
96
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
97 <outputs>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
98 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
99 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
100
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
101 </outputs>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
102
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
103 <help>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
104
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
105 </help>
22d79320085c Uploaded
big-tiandm
parents:
diff changeset
106 </tool>