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comparison siRNA_pipeline.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 #for $j, $s in enumerate( $series )
22 ##rank_of_series=$j
23 -i ${s.input}
24 -tag ${s.tag}
25 #end for
26
27 ## prepare bowtie index
28 #set index_path = ''
29 #if str($reference_genome.source) == "history":
30 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
31 #set index_path = 'genome'
32 #else:
33 #set index_path = $reference_genome.index.fields.path
34 #end if
35
36
37 ## prepare Rfam bowtie index
38 #set rfam_index_path = ''
39 #if str($reference_rfam.source) == "history":
40 bowtie-build "$reference_rfam.own_file" rfam; ln -s $reference_rfam.own_file" rfam.fa;
41 #set rfam_index_path = 'rfam'
42 #else:
43 #set rfam_index_path = $reference_rfam.index.fields.path
44 #end if
45
46
47
48 ## Do or not annotate siRNAs by function
49 #if $params.function_anno == "yes":
50 -nat $params.nat -repeat $params.repeat
51 #end if
52
53 ## Do or not DEG
54 #if $degseq.degseq_analysis == "yes" :
55 -deg $degseq.deg
56 #end if
57
58 -format $format -phred $phred -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v -a $a -n $mapnt -d $d -p $p -l $l -cen $cen -span $span > run.log
59
60 </command>
61
62 <inputs>
63
64 <repeat name="series" title="Series">
65 <param name="input" type="data" label="Raw data file"/>
66 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
67 </repeat>
68
69 <param name="format" type="select" lable="raw data format" multiple="false">
70 <option value="fastq">Raw data is fastq. format</option>
71 <option value="fasta">Raw data is fasta. format</option>
72 </param>
73
74 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
75 <option value="64">Phred+64</option>
76 <option value="33" selected="true">Phred+33</option>
77 </param>
78
79 <conditional name="reference_genome">
80 <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">
81 <option value="indexed">Use a built-in index</option>
82 <option value="history">Use one from the history</option>
83 </param>
84 <when value="indexed">
85 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
86 <options from_data_table="bowtie_indexes">
87 <filter type="sort_by" column="2"/>
88 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
89 </options>
90 </param>
91 </when>
92 <when value="history">
93 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
94 </when>
95 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
96
97 <conditional name="reference_rfam">
98 <param name="source" type="select" label="Will you select a rfam reference from your history or use a built-in index?" help="Built-ins were indexed using default options">
99 <option value="indexed">Use a built-in index</option>
100 <option value="history">Use one from the history</option>
101 </param>
102 <when value="indexed">
103 <param name="index" type="select" label="Select a reference " help="If your rfam of interest is not listed, contact the Galaxy team">
104 <options from_data_table="rfam_bowtie_indexes">
105 <filter type="sort_by" column="2"/>
106 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
107 </options>
108 </param>
109 </when>
110 <when value="history">
111 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
112 </when>
113 </conditional>
114
115 <param name="gff" type="data" label="gff file" />
116 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
117 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
118 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
119 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
120 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
121
122 <param name="p" type="select" lable="cluster method" multiple="false">
123 <option value="F">conventional</option>
124 <option value="T">NIBLES</option>
125 </param>
126 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
127
128
129 <conditional name="params">
130 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
131 <option value="no" selected="true">no</option>
132 <option value="yes">yes</option>
133 </param>
134 <when value="yes">
135 <param name="nat" type="data" label="atural antisense transcripts file" />
136 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
137 </when>
138 </conditional> <!-- params -->
139
140 <param name="cen" type="data" label="centromere file input" />
141 <param name="span" type="integer" value="50000" label="plot span" />
142
143 <conditional name="degseq">
144 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
145 <option value="no" selected="true">no</option>
146 <option value="yes">yes</option>
147 </param>
148 <when value="yes">
149 <param name="deg" type="data" label="file config of de sample" />
150 </when>
151 </conditional>
152
153 </inputs>
154
155 <outputs>
156 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
157 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
158
159 </outputs>
160
161 <help>
162
163 </help>
164 </tool>