Mercurial > repos > big-tiandm > mirplant2
comparison miRPlant.xml @ 49:f008ab2cadc6 draft
Uploaded
author | big-tiandm |
---|---|
date | Wed, 03 Dec 2014 02:03:27 -0500 |
parents | |
children | 7b5a48b972e9 |
comparison
equal
deleted
inserted
replaced
48:28ad3b598670 | 49:f008ab2cadc6 |
---|---|
1 <tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0"> | |
2 <description>tool for plant microRNA analisis</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">miRPlant.pl | |
16 ## Change this to accommodate the number of threads you have available. | |
17 -t \${GALAXY_SLOTS:-4} | |
18 ## Do or not delet rfam mapped tags | |
19 #if $params.delet_rfam == "yes": | |
20 -D | |
21 #end if | |
22 -path \$SCRIPT_PATH | |
23 | |
24 #for $j, $s in enumerate( $series ) | |
25 ##rank_of_series=$j | |
26 -i ${s.input} | |
27 -tag ${s.tag} | |
28 #end for | |
29 | |
30 -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log | |
31 </command> | |
32 | |
33 <inputs> | |
34 | |
35 <repeat name="series" title="Series"> | |
36 <param name="input" type="data" label="Raw data"/> | |
37 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/> | |
38 </repeat> | |
39 | |
40 <conditional name="params"> | |
41 <param name="delet_rfam" type="select" label="delet rfam mapped reads"> | |
42 <option value="yes" selected="true">yes</option> | |
43 <option value="no">no</option> | |
44 </param> | |
45 </conditional> <!-- params --> | |
46 | |
47 <!--param name="input" format="tabular" type="data" label="input config file" /--> | |
48 | |
49 <param name="format" type="select" lable="raw data format" multiple="false"> | |
50 <option value="fastq">Raw data is fastq. format</option> | |
51 <option value="fasta">Raw data is fasta. format</option> | |
52 </param> | |
53 | |
54 <param name="gfa" type="data" label="genome sequence fasta file"/> | |
55 <!--param type="data" name="index" label="genome sequence bowtie index"/--> | |
56 <param name="mat" type="data" label="mature microRNA sequence file" /> | |
57 <param name="pre" type="data" label="precursor microRNA sequence fie" /> | |
58 <param name="rfam" type="data" label="rfam sequence file" /> | |
59 <!--param type="data" name="idx2" label="rfam sequence bowtie index " --> | |
60 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> | |
61 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> | |
62 <param name="min" type="integer" value="19" label="minimum microRNA length" /> | |
63 <param name="max" type="integer" value="28" label="maximum microRNA length" /> | |
64 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" /> | |
65 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" /> | |
66 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" /> | |
67 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/> | |
68 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> | |
69 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" /> | |
70 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" /> | |
71 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" /> | |
72 </inputs> | |
73 | |
74 <outputs> | |
75 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/> | |
76 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/> | |
77 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/> | |
78 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/> | |
79 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/> | |
80 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/> | |
81 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/> | |
82 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/> | |
83 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/> | |
84 </outputs> | |
85 | |
86 <help> | |
87 | |
88 </help> | |
89 </tool> |