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comparison preProcess.xml @ 47:c75593f79aa9 draft

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author big-tiandm
date Wed, 03 Dec 2014 01:54:29 -0500
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46:ca05d68aca13 47:c75593f79aa9
1 <tool id="preprocess" name="preProcess" veision="1.0.0">
2 <description>tool for Raw data preprocess analisis, including 3' adapter triming, reads collaping, genome mapping and rfam non-miRNA 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">miRPlant.pl
16 ## Change this to accommodate the number of threads you have available.
17 -t \${GALAXY_SLOTS:-4}
18 -path \$SCRIPT_PATH
19
20 #for $j, $s in enumerate( $series )
21 ##rank_of_series=$j
22 -i ${s.input}
23 -tag ${s.tag}
24 #end for
25
26 ## Do or not annotate rfam non-miRNA RNAs
27 #if $params.annotate_rfam == "yes":
28 -rfam $rfam
29 #end if
30
31 ## prepare bowtie index
32 #set index_path = ''
33 #if str($reference_genome.source) == "history":
34 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
35 #set index_path = 'genome'
36 #else:
37 #set index_path = $reference_genome.index.fields.path
38 #end if
39
40 -format $format -gfa ${index_path}.fa -idx $index_path -a $a -M $mapnt -min $min -max $max -mis $mismatch -v $v > run.log
41 </command>
42
43 <inputs>
44
45 <repeat name="series" title="Series">
46 <param name="input" type="data" label="Raw data"/>
47 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
48 </repeat>
49
50 <!--param name="input" format="tabular" type="data" label="input config file" /-->
51
52 <param name="format" type="select" lable="raw data format" multiple="false">
53 <option value="fastq">Raw data is fastq. format</option>
54 <option value="fasta">Raw data is fasta. format</option>
55 </param>
56
57 <!-- reference genome -->
58 <conditional name="reference_genome">
59 <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">
60 <option value="indexed">Use a built-in index</option>
61 <option value="history">Use one from the history</option>
62 </param>
63 <when value="indexed">
64 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
65 <options from_data_table="bowtie_indexes">
66 <filter type="sort_by" column="2"/>
67 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
68 </options>
69 </param>
70 </when>
71 <when value="history">
72 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
73 </when>
74 </conditional>
75
76 <!--param name="gfa" type="data" label="genome sequence fasta file"/-->
77 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
78 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
79 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
80 <param name="min" type="integer" value="19" label="minimum microRNA length" />
81 <param name="max" type="integer" value="28" label="maximum microRNA length" />
82 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
83
84 <conditional name="params">
85 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
86 <option value="yes" selected="true">yes</option>
87 <option value="no">no</option>
88 </param>
89 <when value="yes">
90 <param name="rfam" type="data" label="rfam sequence file" />
91 <!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
92 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
93 </when>
94 </conditional> <!-- params -->
95
96 </inputs>
97
98 <outputs>
99 <data format="html" name="preprocess result" from_work_dir="preProcess/preprocessResult.html" label="${tool.name} on ${on_string}: preprocess result"/>
100
101 <data format="txt" name="clean FASTA data" from_work_dir="preProcess/preProcess_clean/collapse_reads_$min_$max.fa" label="${tool.name} on ${on_string}: clean FASTA data"/>
102
103 <data format="txt" name="genome mapping result" from_work_dir="preProcess/genome_match/genome_mapped.bwt" label="${tool.name} on ${on_string}: genome mapping result"/>
104 <data format="txt" name="genome mapped FASTA reads" from_work_dir="preProcess/genome_match/genome_mapped.fa" label="${tool.name} on ${on_string}: genome mapped FASTA reads"/>
105
106 <data format="txt" name="Rfam mapping result" from_work_dir="preProcess/rfam_match/rfam_mapped.bwt" label="${tool.name} on ${on_string}: Rfam mapping result">
107 <filter>(params['annotate_rfam'] == 'Yes')</filter>
108 </data>
109 <data format="txt" name="Rfam mapped FASTA file" from_work_dir="preProcess/rfam_match/rfam_mapped.fa" label="${tool.name} on ${on_string}: Rfam mapped FASTA file">
110 <filter>(params['annotate_rfam'] == 'Yes')</filter>
111 </data>
112 <data format="txt" name="Rfam not mapped FASTA file" from_work_dir="preProcess/rfam_match/rfam_not_mapped.fa" label="${tool.name} on ${on_string}: Rfam not mapped FASTA file">
113 <filter>(params['annotate_rfam'] == 'Yes')</filter>
114 </data>
115 </outputs>
116
117 <help>
118
119 </help>
120 </tool>