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comparison siRNA_pipeline.xml @ 0:87fe81de0931 draft default tip

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author bigrna
date Sun, 04 Jan 2015 02:47:25 -0500
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1 <tool id="plant_sirna_pipeline_v1" name="siRNA_pipeline" veision="1.0.0">
2 <description>Program for plant siRNA analysis (rawdata preprocess -> genome alignment -> non-coding annotate -> siRNA analysis)</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 #set index_path = $reference_genome.own_file
31 -g $index_path
32 #else:
33 #set index_path = $reference_genome.index.fields.path
34 -g ${index_path}.fa -idx $index_path
35 #end if
36
37
38 ## prepare Rfam bowtie index
39 #set rfam_index_path = ''
40 #if str($reference_rfam.source) == "history":
41 #set rfam_index_path = $reference_rfam.own_file
42 -rfam $rfam_index_path -v $v
43 #else:
44 #set rfam_index_path = $reference_rfam.index.fields.path
45 -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v
46 #end if
47
48
49
50 ## Do or not annotate siRNAs by function
51 #if $params.function_anno == "yes":
52
53 ## prepare bowtie index
54 #set nat_path = ''
55 #if str($params.nat_file.source) == "history":
56 #set nat_path = $params.nat_file.nat
57
58 #else:
59 #set nat_path = $params.nat_file.index.fields.path
60 #end if
61
62 ## prepare bowtie index
63 #set repeat_path = ''
64 #if str($params.repeat_file.source) == "history":
65 #set repeat_path = $params.repeat_file.repeat
66
67 #else:
68 #set repeat_path = $params.repeat_file.index.fields.path
69 #end if
70
71
72 -nat $nat_path -repeat $repeat_path
73 #end if
74
75 ## Do or not DEG
76 #if $degseq.degseq_analysis == "yes" :
77 -deg $degseq.deg
78 #end if
79
80 -format $format -phred $phred -f $gff -mis $mis -a $a -n $mapnt -d $d -p $p -l $l -cen $cen -span $span > run.log
81
82 </command>
83
84 <inputs>
85
86 <repeat name="series" title="Raw sequence data file">
87 <param name="input" type="data" label="Raw data file"/>
88 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
89 </repeat>
90
91 <param name="format" type="select" label="raw data format" multiple="false">
92 <option value="fastq">Raw data is fastq. format</option>
93 <option value="fasta">Raw data is fasta. format</option>
94 </param>
95
96 <param name="phred" type="select" label="input quals are Phred+64 or Phred+33" multiple="false">
97 <option value="64">Phred+64</option>
98 <option value="33" selected="true">Phred+33</option>
99 </param>
100
101 <conditional name="reference_genome">
102 <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">
103 <option value="indexed">Use a built-in index</option>
104 <option value="history">Use one from the history</option>
105 </param>
106 <when value="indexed">
107 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
108 <options from_data_table="bowtie_indexes">
109 <filter type="sort_by" column="2"/>
110 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
111 </options>
112 </param>
113 </when>
114 <when value="history">
115 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
116 </when>
117 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
118
119 <conditional name="reference_rfam">
120 <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">
121 <option value="indexed">Use a built-in index</option>
122 <option value="history">Use one from the history</option>
123 </param>
124 <when value="indexed">
125 <param name="index" type="select" label="Select a non-coding reference " help="If your rfam of interest is not listed, contact the Galaxy team">
126 <options from_data_table="rfam_bowtie_indexes">
127 <filter type="sort_by" column="2"/>
128 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
129 </options>
130 </param>
131 </when>
132 <when value="history">
133 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
134 </when>
135 </conditional>
136
137 <param name="gff" type="data" label="gff file" />
138 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
139 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for non-coding alignment"/>
140 <param name="a" type="text" value="TGGAATTCTCGGGTGCCAAGG" label="3' adapter sequence" />
141 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
142 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
143
144 <param name="p" type="select" label="siRNA cluster identify method" multiple="false">
145 <option value="F">conventional</option>
146 <option value="T">NIBLES</option>
147 </param>
148 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
149
150
151 <conditional name="params">
152 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
153 <option value="no" selected="true">no</option>
154 <option value="yes">yes</option>
155 </param>
156 <when value="yes">
157
158
159 <conditional name="nat_file">
160 <param name="source" type="select" label="Will you select a atural antisense transcripts file from your history ?" help="down load from ***">
161 <option value="indexed">Use a built-in file</option>
162 <option value="history">Use one from the history</option>
163 </param>
164 <when value="indexed">
165 <param name="index" type="select" label="Select a atural antisense transcripts file" help="If your species of interest is not listed, contact the Galaxy team">
166 <options from_data_table="nat_annotate">
167 <filter type="sort_by" column="2"/>
168 <validator type="no_options" message="No files are available for the selected input dataset"/>
169 </options>
170 </param>
171 </when>
172 <when value="history">
173 <param name="nat" type="data" format="txt" metadata_name="dbkey" label="atural antisense transcripts file" />
174 </when>
175 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
176
177 <conditional name="repeat_file">
178 <param name="source" type="select" label="Will you select a repeat information file from your history ?" help="down load from ***">
179 <option value="indexed">Use a built-in file</option>
180 <option value="history">Use one from the history</option>
181 </param>
182 <when value="indexed">
183 <param name="index" type="select" label="Select a repeat information file" help="If your species of interest is not listed, contact the Galaxy team">
184 <options from_data_table="repeat_annotate">
185 <filter type="sort_by" column="2"/>
186 <validator type="no_options" message="No files are available for the selected input dataset"/>
187 </options>
188 </param>
189 </when>
190 <when value="history">
191 <param name="repeat" type="data" metadata_name="dbkey" label="repeat information file out of Repeatmasker" />
192 </when>
193 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
194 </when>
195 </conditional> <!-- params -->
196
197 <param name="cen" type="data" label="centromere file input" />
198 <param name="span" type="integer" value="50000" label="plot span" />
199
200 <conditional name="degseq">
201 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
202 <option value="no" selected="true">no</option>
203 <option value="yes">yes</option>
204 </param>
205 <when value="yes">
206 <param name="deg" type="data" label="file config of de sample" />
207 </when>
208 </conditional>
209
210 </inputs>
211
212 <outputs>
213 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
214 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
215
216 </outputs>
217
218 <help>
219
220 </help>
221 </tool>