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comparison signature.xml @ 10:68ee7c84d498 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
author artbio
date Tue, 07 Jan 2020 06:59:56 -0500
parents 59ee49bfb7bb
children 8d3ca9652a5b
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9:59ee49bfb7bb 10:68ee7c84d498
1 <tool id="signature" name="Small RNA Signatures" version="3.2.0"> 1 <tool id="signature" name="Small RNA Signatures" version="3.2.1">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 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> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.6.1=r351h6115d3f_0">r-optparse</requirement> 6 <requirement type="package" version="1.6.1=r351h6115d3f_0">r-optparse</requirement>
87 87
88 **What it does** 88 **What it does**
89 89
90 Compute small RNA (piRNA, siRNA, ...) signatures. 90 Compute small RNA (piRNA, siRNA, ...) signatures.
91 91
92 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated the z-scores, 92 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores,
93 and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. 93 and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores.
94 94
95 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads 95 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads
96 when these reads can be aligned at multiple positions in the genome. The two values are equal only 96 when these reads can be aligned at multiple positions in the genome. The two values are equal only
97 when the analysis is restricted to uniquely mapping reads. 97 when the analysis is restricted to uniquely mapping reads.
98 98
99 Options set the min and max size of both the query small rna class and the target small rna class, 99 Options set the min and max size of both the query small rna class and the target small rna class,
100 the range over which to compute the signatures, and whether the signatures should be reported at 100 the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at
101 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 101 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes
102 for piRNA and siRNA signatures, see `Antoniewski (2014)`_. 102 for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
103 103
104 .. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171 104 .. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
105 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12 105 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
108 108
109 A **sorted** BAM alignment file. 109 A **sorted** BAM alignment file.
110 110
111 **Outputs** 111 **Outputs**
112 112
113 **Global**: The number of pairs founds, the ping-pong signal and the associated z-scores 113 **Global**: The number of pairs found, the ping-pong signal and the associated z-scores
114 are computed at genome-wide level and returned in a pdf file. 114 are computed at genome-wide level and returned in a pdf file.
115 115
116 **Lattice**: The number of pairs founds, the ping-pong signals and the associated z-scores 116 **Lattice**: The number of pairs found, the ping-pong signals and the associated z-scores
117 are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph. 117 are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.
118 118
119 119
120 </help> 120 </help>
121 <citations> 121 <citations>