Mercurial > repos > nikhil-joshi > mirdeep2_and_targetspy
comparison mirdeep2/mirdeep2.xml @ 0:5b9519f4b165
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author | nikhil-joshi |
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date | Mon, 19 Sep 2011 19:04:41 -0400 |
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-1:000000000000 | 0:5b9519f4b165 |
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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> |