|
50
|
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="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_001">Boost-Graph</requirement>
|
|
|
13 </requirements>
|
|
|
14
|
|
|
15 <command interpreter="perl">siRNA_pipeline.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 ## prepare bowtie index
|
|
|
22 #set index_path = ''
|
|
|
23 #if str($reference_genome.source) == "history":
|
|
|
24 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
|
|
|
25 #set index_path = 'genome'
|
|
|
26 #else:
|
|
|
27 #set index_path = $reference_genome.index.fields.path
|
|
|
28 #end if
|
|
|
29
|
|
|
30
|
|
|
31 ## Do or not annotate siRNAs by function
|
|
|
32 #if $params.function_anno == "yes":
|
|
|
33 -nat $params.nat -repeat $params.repeat
|
|
|
34 #end if
|
|
|
35
|
|
|
36 ## Do or not DEG
|
|
|
37 #if $degseq.degseq_analysis == "yes" :
|
|
|
38 -deg $degseq.deg
|
|
|
39 #end if
|
|
|
40
|
|
|
41 -i $reads -config $config -n $hits -format $format -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -d $d -p $p -l $l -cen $cen -span $span > run.log
|
|
|
42
|
|
|
43 </command>
|
|
|
44
|
|
|
45 <inputs>
|
|
|
46
|
|
|
47 <param name="config" type="data" label="Raw data configs file" />
|
|
|
48 <param name="reads" type="data" label="Input Fasta. file of candidate microRNA sequence" />
|
|
|
49
|
|
|
50 <param name="format" type="select" lable=" data format" multiple="false">
|
|
|
51 <option value="fastq">Raw data is fastq. format</option>
|
|
|
52 <option value="fasta">Raw data is fasta. format</option>
|
|
|
53 </param>
|
|
|
54
|
|
|
55
|
|
|
56 <conditional name="reference_genome">
|
|
|
57 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
|
|
|
58 <option value="indexed">Use a built-in index</option>
|
|
|
59 <option value="history">Use one from the history</option>
|
|
|
60 </param>
|
|
|
61 <when value="indexed">
|
|
|
62 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
|
|
|
63 <options from_data_table="bowtie_indexes">
|
|
|
64 <filter type="sort_by" column="2"/>
|
|
|
65 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
|
|
|
66 </options>
|
|
|
67 </param>
|
|
|
68 </when>
|
|
|
69 <when value="history">
|
|
|
70 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
|
|
|
71 </when>
|
|
|
72 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
|
|
|
73
|
|
|
74
|
|
|
75 <param name="gff" type="data" label="gff file" />
|
|
|
76 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
|
|
|
77 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
|
|
|
78 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
|
|
|
79
|
|
|
80 <param name="p" type="select" lable="cluster method" multiple="false">
|
|
|
81 <option value="F">conventional</option>
|
|
|
82 <option value="T">NIBLES</option>
|
|
|
83 </param>
|
|
|
84 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
|
|
|
85
|
|
|
86
|
|
|
87 <conditional name="params">
|
|
|
88 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
|
|
|
89 <option value="no" selected="true">no</option>
|
|
|
90 <option value="yes">yes</option>
|
|
|
91 </param>
|
|
|
92 <when value="yes">
|
|
|
93 <param name="nat" type="data" label="atural antisense transcripts file" />
|
|
|
94 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
|
|
|
95 </when>
|
|
|
96 </conditional> <!-- params -->
|
|
|
97
|
|
|
98 <param name="cen" type="data" label="centromere file input" />
|
|
|
99 <param name="span" type="integer" value="50000" label="plot span" />
|
|
|
100
|
|
|
101 <conditional name="degseq">
|
|
|
102 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
|
|
|
103 <option value="no" selected="true">no</option>
|
|
|
104 <option value="yes">yes</option>
|
|
|
105 </param>
|
|
|
106 <when value="yes">
|
|
|
107 <param name="deg" type="data" label="file config of de sample" />
|
|
|
108 </when>
|
|
|
109 </conditional>
|
|
|
110
|
|
|
111 </inputs>
|
|
|
112
|
|
|
113 <outputs>
|
|
|
114 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
|
|
|
115 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
|
|
|
116
|
|
|
117 </outputs>
|
|
|
118
|
|
|
119 <help>
|
|
|
120
|
|
|
121 </help>
|
|
|
122 </tool>
|
