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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
author artbio
date Mon, 28 Aug 2017 09:29:47 -0400
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1 <tool id="signature" name="Small RNA Signatures" version="3.0.0">
2 <description />
3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
7 <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
8 <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
9 </requirements>
10 <stdio>
11 <exit_code range="1:" level="fatal" description="Tool exception" />
12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[
14 samtools index '$input' &&
15 python '$__tool_directory__'/signature.py
16 --input '$input'
17 --minquery '$minquery'
18 --maxquery '$maxquery'
19 --mintarget '$mintarget'
20 --maxtarget '$maxtarget'
21 --minscope '$minscope'
22 --maxscope '$maxscope'
23 --output_h '$h_dataframe'
24 --output_z '$z_dataframe' &&
25 Rscript '$__tool_directory__'/signature.r
26 --h_dataframe '$h_dataframe'
27 --z_dataframe '$z_dataframe'
28 --plot_method '$plot_method'
29 --pdf '$pdf'
30 --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
31 ]]></command>
32 <inputs>
33 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
34 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
35 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
36 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
37 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
38 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
39 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
40 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
41 <option selected="True" value="global">Global</option>
42 <option value="lattice">Lattice</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data format="tabular" label="z-signature data frame" name="z_dataframe">
47 <actions>
48 <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />
49 </actions>
50 </data>
51 <data format="tabular" label="h-signature data frame" name="h_dataframe">
52 <actions>
53 <action name="column_names" type="metadata" default="Chromosome,Overlap,overlap_probability,z-score" />
54 </actions>
55 </data>
56 <data format="pdf" label="Overlap probabilities" name="pdf" />
57 </outputs>
58 <tests>
59 <test>
60 <param ftype="bam" name="input" value="sr_bowtie.bam" />
61 <param name="minquery" value="23" />
62 <param name="maxquery" value="29" />
63 <param name="mintarget" value="23" />
64 <param name="maxtarget" value="29" />
65 <param name="minscope" value="5" />
66 <param name="maxscope" value="15" />
67 <param name="plot_method" value="global" />
68 <output file="h.tab" ftype="tabular" name="h_dataframe" />
69 <output file="z.tab" ftype="tabular" name="z_dataframe" />
70 <output file="global.pdf" ftype="pdf" name="pdf" />
71 </test>
72 <test>
73 <param ftype="bam" name="input" value="sr_bowtie.bam" />
74 <param name="minquery" value="23" />
75 <param name="maxquery" value="29" />
76 <param name="mintarget" value="23" />
77 <param name="maxtarget" value="29" />
78 <param name="minscope" value="5" />
79 <param name="maxscope" value="15" />
80 <param name="plot_method" value="lattice" />
81 <output file="h.tab" ftype="tabular" name="h_dataframe" />
82 <output file="z.tab" ftype="tabular" name="z_dataframe" />
83 <output file="lattice.pdf" ftype="pdf" name="pdf" />
84 </test>
85 </tests>
86 <help>
87
88 **What it does**
89
90 Compute small RNA (piRNA, siRNA, ...) signatures.
91
92 This tool computes (i) the number of pairs by overlap classes (in nt) and associated the z-scores,
93 and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores.
94 Options set the min and max size of both the query small rna class and the target small rna class,
95 the range over which to compute the signatures, and whether the signatures should be reported at
96 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes
97 for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
98
99 .. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
100 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
101
102 **Input**
103
104 A **sorted** BAM alignment file.
105
106 **Outputs**
107
108 **Global**: The number of pairs founds, the ping-pong signal and the associated z-scores
109 are computed at genome-wide level and returned in a pdf file.
110
111 **Lattice**: The number of pairs founds, the ping-pong signals and the associated z-scores
112 are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.
113
114
115 </help>
116 <citations>
117 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
118 </citations>
119 </tool>