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comparison microRNA.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="micrornas" name="microRNA" veision="1.0.0">
2 <description>Plant 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="2.59">SVG</requirement>
10 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
11 </requirements>
12
13 <!--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-->
14
15 <command interpreter="perl">microRNA.pl
16 ## Change this to accommodate the number of threads you have available.
17 -t \${GALAXY_SLOTS:-4}
18 -path \$SCRIPT_PATH
19
20
21 ## Do or not annotate known microRNAs
22 #if $params.known_microRNA == "yes":
23 -pre $pre -mat $mat
24 #end if
25
26 ## prepare bowtie index
27 #set index_path = ''
28 #if str($reference_genome.source) == "history":
29 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
30 #set index_path = 'genome'
31 #else:
32 #set index_path = $reference_genome.index.fields.path
33 #end if
34
35
36 -gfa ${index_path}.fa -idx $index_path -mis $mismatch -i $config -fa $reads -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
37 </command>
38
39 <inputs>
40
41 <!-- reference genome -->
42 <conditional name="reference_genome">
43 <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">
44 <option value="indexed">Use a built-in index</option>
45 <option value="history">Use one from the history</option>
46 </param>
47 <when value="indexed">
48 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
49 <options from_data_table="bowtie_indexes">
50 <filter type="sort_by" column="2"/>
51 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
52 </options>
53 </param>
54 </when>
55 <when value="history">
56 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
57 </when>
58 </conditional>
59
60 <conditional name="params">
61 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
62 <option value="yes" selected="true">yes</option>
63 <option value="no">no</option>
64 </param>
65 <when value="yes">
66 <param name="mat" type="data" label="mature microRNA sequence file" />
67 <param name="pre" type="data" label="precursor microRNA sequence fie" />
68 </when>
69 </conditional> <!-- params -->
70
71 <param name="config" type="data" label="Raw data configs file" />
72 <param name="reads" type="data" label="Input Fasta. file of candidate microRNA sequence" />
73
74
75 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
76 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
77 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
78 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
79 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
80 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
81 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
82
83 </inputs>
84
85 <outputs>
86 <data format="txt" name="known microRNA express list" from_work_dir="miRNA_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
87 <filter>(params['known_microRNA'] == 'Yes')</filter>
88 </data>
89 <data format="txt" name="known microRNA express alignment" from_work_dir="miRNA_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
90 <filter>(params['known_microRNA'] == 'Yes')</filter>
91 </data>
92 <data format="txt" name="known microRNA moRs result" from_work_dir="miRNA_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
93 <filter>(params['known_microRNA'] == 'Yes')</filter>
94 </data>
95 <data format="txt" name="known microRNA precursor file" from_work_dir="miRNA_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
96 <filter>(params['known_microRNA'] == 'Yes')</filter>
97 </data>
98 <data format="txt" name="known microRNA mature file" from_work_dir="miRNA_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
99 <filter>(params['known_microRNA'] == 'Yes')</filter>
100 </data>
101 <data format="txt" name="novel microRNA express list" from_work_dir="miRNA_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
102 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRNA_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
103 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRNA_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
104 <data format="txt" name="non-microRNA sequence FASTA file" from_work_dir="miRNA_out/non_miRNA_reads.fa" label="${tool.name} on ${on_string}: Sequence FASTA file of non-microRNA tags"/>
105
106 </outputs>
107
108 <help>
109
110 </help>
111 </tool>