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comparison siRNA.xml @ 50:7b5a48b972e9 draft

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author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
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49:f008ab2cadc6 50:7b5a48b972e9
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>