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comparison mirdeep2.xml @ 0:17e442abb3de draft default tip

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author david-hoover
date Wed, 23 Jul 2014 10:27:07 -0400
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1 <tool id="mirdeep2" name="miRDeep2">
2 <description>Find miRNA candidates using output from mapping step</description>
3
4 <requirements>
5 <requirement type="perl-module">mirdeep2_wrapper.pl</requirement>
6 </requirements>
7
8 <command interpreter="perl">
9 ./mirdeep2_wrapper.pl $collapsed_reads $bowtie_index $bowtie_index.extra_files_path $arf_file $mirna_ref $mirna_other $precursors "$html_output.files_path" "$collapsed_reads.name" $csv_output $html_output $survey_output $mrd_output
10
11 #if str($min_stack_height) != '':
12 -a $min_stack_height
13 #end if
14
15 #if str($max_num_precursors) != '':
16 -g $max_num_precursors
17 #end if
18
19 #if str($min_score_cutoff) != '':
20 -b $min_score_cutoff
21 #end if
22
23 #if str($disable_randfold) == 'disable_randfold_true':
24 -c
25 #end if
26
27 #if str($ucsc_genome) != 'None':
28 -t $ucsc_genome
29 #end if
30
31 #if str($star_seq) != 'None':
32 -s $star_seq
33 #end if
34 </command>
35
36 <inputs>
37 <param format="fasta" type="data" name="collapsed_reads" optional="false" label="Collapsed reads fasta file" help="Collapsed read fasta file outputted from mapping step"/>
38
39 <param format="bowtie_html_index" type="data" name="bowtie_index" optional="false" label="Bowtie indexed reference" help="Select the bowtie-build run, NOT the fasta reference file you indexed"/>
40
41 <param format="arf" type="data" name="arf_file" optional="false" label="ARF file from mapping step"/>
42
43 <param format="fasta" type="data" name="mirna_ref" optional="true" label="Known miRBase miRNA sequences in fasta format (optional)" help="If used, these should be the known mature sequences for the species being analyzed"/>
44
45 <param format="fasta" type="data" name="mirna_other" optional="true" label="Known related miRBase miRNA sequences in fasta format (optional)" help="If used, these should be pooled known mature sequences for 1-5 species closely related to the species being analyzed"/>
46
47 <param format="fasta" type="data" name="precursors" optional="true" label="Known miRBase miRNA precursors in fasta format (optional)" help="If used, these should be the known precursor sequences for the species being analyzed"/>
48
49 <param format="fasta" type="data" name="star_seq" optional="true" label="Known miRBase miRNA star sequences in fasta format (optional)" help="If used, these should be the known star sequences for the species being analyzed"/>
50
51 <param name="min_stack_height" value="" type="integer" optional="true" label="Minimum read stack height that triggers analysis (optional)" help="Using this option disables automatic estimation of the optimal value and all detected precursors are analyzed"/>
52
53 <param name="max_num_precursors" value="50000" type="integer" label="Maximum number of precursors to analyze when automatic excision gearing is used (default 50000)" help="If set to -1 all precursors will be analyzed"/>
54
55 <param name="min_score_cutoff" value="0" type="integer" label="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table" help="This score cut-off is by default 0"/>
56
57 <param name="disable_randfold" type="boolean" truevalue="disable_randfold_true" falsevalue="disable_randfold_false" checked="false" label="Disable randfold analysis" help="Runs faster but with less accurate results"/>
58
59 <param name="ucsc_genome" type="select" optional="true" label="Species being analyzed - this is used to link to the appropriate UCSC browser entry (optional)">
60 <options from_file="ucsc_browser_species.txt">
61 <column name="value" index="0"/>
62 </options>
63 </param>
64 </inputs>
65
66 <outputs>
67 <data format="csv" name="csv_output" label="miRNA CSV output of ${tool.name} on ${on_string}"/>
68 <data format="html" name="html_output" label="miRNA HTML output of ${tool.name} on ${on_string}"/>
69 <data format="csv" name="survey_output" label="miRNA prediction accuracy spreadsheet of ${tool.name} on ${on_string}"/>
70 <data format="txt" name="mrd_output" label="miRNA hairpins of ${tool.name} on ${on_string}"/>
71 </outputs>
72
73 <help>
74 miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.
75
76 The output files produced are:
77
78 result.html: a html table giving an overview of novel and known miRNAs detected in the data. The table is hyperlinked to pdfs showing the signature and structure of each hairpin.
79
80 result.csv: spread-sheet format of results.html
81
82 survey.csv: spread-sheet of prediction accuracy for all score-cutoffs between -10 and 10.
83
84 output.mrd: text output of the reported hairpins.
85
86 </help>
87 </tool>