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comparison microRNA_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_microRNA_v1" name="microRNA_pipeline" veision="1.0.0">
2 <description>Program for plant microRNA analysis (rawdata preprocess -> genome mapping -> non-coding RNA(exclude miRNAs) annotation -> microRNA analysis)</description>
3
4 <requirements>
5 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
6 <requirement type="package" version="0.12.7">bowtie</requirement>
7 <requirement type="set_environment">SCRIPT_PATH</requirement>
8 <!--requirement type="package" version="3.0.1">R</requirement!-->
9 <requirement type="package" version="1.96">threads</requirement>
10 <requirement type="package" version="2.59">SVG</requirement>
11 <!--requirement type="package" version="0.228">parent</requirement-->
12 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
13 </requirements>
14
15 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
16
17 <command interpreter="perl">microRNA_pipeline.pl
18 ## Change this to accommodate the number of threads you have available.
19 -t \${GALAXY_SLOTS:-4}
20 -path \$SCRIPT_PATH
21
22 #for $j, $s in enumerate( $series )
23 ##rank_of_series=$j
24 -i ${s.input}
25 -tag ${s.tag}
26 #end for
27
28 ## prepare bowtie index
29 #set index_path = ''
30 #if str($reference_genome.source) == "history":
31 #####bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
32 #set index_path = $reference_genome.own_file
33 -gfa $index_path
34 #else:
35 #set index_path = $reference_genome.index.fields.path
36 -gfa ${index_path}.fa -idx $index_path
37 #end if
38
39
40 ## Do or not annotate rfam non-miRNA RNAs
41 #if $params.annotate_rfam == "yes":
42
43 ## prepare Rfam bowtie index
44 #set rfam_index_path = ''
45 #if str($params.reference_rfam.source) == "history":
46 ######## bowtie-build "$params.reference_rfam.own_file" rfam; ln -s "$params.reference_rfam.own_file" rfam.fa;
47 #set rfam_index_path = $params.reference_rfam.own_file
48 -rfam $rfam_index_path
49 #else:
50 #set rfam_index_path = $params.reference_rfam.index.fields.path
51 -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path
52 #end if
53
54 -v $params.v
55 ## Do or not delete rfam mapped tags
56 #if $params.delete_rfam == "yes":
57 -D
58 #end if
59 #end if
60
61
62 ## Do or not annotate known microRNAs
63 #if $mirbase.known_microRNA == "yes":
64 -pre $mirbase.pre -mat $mirbase.mat
65 #end if
66
67
68 -format $format -phred $phred -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
69 </command>
70
71 <inputs>
72
73 <repeat name="series" title="Raw sequence data">
74 <param name="input" type="data" label="Raw data"/>
75 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
76 </repeat>
77
78 <param name="format" type="select" label="Raw data format" multiple="false">
79 <option value="fastq">Raw data is fastq. format</option>
80 <option value="fasta">Raw data is fasta. format</option>
81 </param>
82
83 <param name="phred" type="select" label="Input quals are Phred+64 or Phred+33" multiple="false">
84 <option value="64">Phred+64</option>
85 <option value="33" selected="true">Phred+33</option>
86 </param>
87
88 <conditional name="reference_genome">
89 <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">
90 <option value="indexed">Use a built-in index</option>
91 <option value="history">Use one from the history</option>
92 </param>
93 <when value="indexed">
94 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
95 <options from_data_table="bowtie_indexes">
96 <filter type="sort_by" column="2"/>
97 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
98 </options>
99 </param>
100 </when>
101 <when value="history">
102 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
103 </when>
104 </conditional>
105
106 <conditional name="params">
107 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
108 <option value="yes" selected="true">yes</option>
109 <option value="no">no</option>
110 </param>
111 <when value="yes">
112 <!--param name="rfam" type="data" label="rfam sequence file" /-->
113 <conditional name="reference_rfam">
114 <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">
115 <option value="indexed">Use a built-in index</option>
116 <option value="history">Use one from the history</option>
117 </param>
118 <when value="indexed">
119 <param name="index" type="select" label="Select a non-coding RNA reference" help="If your reference of interest is not listed, contact the Galaxy team">
120 <options from_data_table="rfam_bowtie_indexes">
121 <filter type="sort_by" column="2"/>
122 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
123 </options>
124 </param>
125 </when>
126 <when value="history">
127 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
128 </when>
129 </conditional>
130
131 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
132
133 <param name="delete_rfam" type="select" label="delet rfam mapped reads">
134 <option value="yes" selected="true">yes</option>
135 <option value="no">no</option>
136 </param>
137 </when>
138
139 </conditional>
140
141 <conditional name="mirbase">
142 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
143 <option value="yes" selected="true">yes</option>
144 <option value="no">no</option>
145 </param>
146 <when value="yes">
147 <param name="mat" type="data" label="mature microRNA sequence file" />
148 <param name="pre" type="data" label="precursor microRNA sequence file" />
149 </when>
150
151 </conditional>
152
153
154 <param name="a" type="text" value="TGGAATTCTCGGGTGCCAAGG" label="3' adapter sequence" />
155 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
156 <param name="min" type="integer" value="19" label="minimum microRNA length" />
157 <param name="max" type="integer" value="28" label="maximum microRNA length" />
158 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
159 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
160 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
161 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
162 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
163 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
164 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
165 </inputs>
166
167 <outputs>
168 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
169 <filter>(mirbase['known_microRNA'] == 'yes')</filter>
170 </data>
171 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
172 <filter>(mirbase['known_microRNA'] == 'yes')</filter>
173 </data>
174 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
175 <filter>(mirbase['known_microRNA'] == 'yes')</filter>
176 </data>
177 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
178 <filter>(mirbase['known_microRNA'] == 'yes')</filter>
179 </data>
180 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
181 <filter>(mirbase['known_microRNA'] == 'yes')</filter>
182 </data>
183 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
184 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
185 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
186 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
187 </outputs>
188
189 <help>
190
191 </help>
192 </tool>