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comparison signature.xml @ 12:aa5e2c64dff8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
author artbio
date Sat, 22 Oct 2022 23:49:52 +0000
parents 8d3ca9652a5b
children 124f404b0fe7
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11:8d3ca9652a5b 12:aa5e2c64dff8
1 <tool id="signature" name="Small RNA Signatures" version="3.3>"> 1 <tool id="signature" name="Small RNA Signatures" version="3.4.1>">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.13=h8c37831_0">samtools</requirement> 4 <requirement type="package" version="1.23.4">numpy</requirement>
5 <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement> 5 <requirement type="package" version="0.18.0">pysam</requirement>
6 <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement> 6 <requirement type="package" version="1.7.3">r-optparse</requirement>
7 <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement> 7 <requirement type="package" version="0.6_30">r-latticeextra</requirement>
8 <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement> 8 <requirement type="package" version="2.3">r-gridextra</requirement>
9 <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement>
10 </requirements> 9 </requirements>
11 <stdio> 10 <stdio>
12 <exit_code range="1:" level="fatal" description="Tool exception" /> 11 <exit_code range="1:" level="fatal" description="Tool exception" />
13 </stdio> 12 </stdio>
14 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
15 samtools index '$input' && 14 ln -f -s $input.metadata.bam_index input.bam.bai &&
15 ln -s $input input.bam &&
16 python '$__tool_directory__'/signature.py 16 python '$__tool_directory__'/signature.py
17 --input '$input' 17 --input input.bam
18 --minquery '$minquery' 18 --minquery '$minquery'
19 --maxquery '$maxquery' 19 --maxquery '$maxquery'
20 --mintarget '$mintarget' 20 --mintarget '$mintarget'
21 --maxtarget '$maxtarget' 21 --maxtarget '$maxtarget'
22 --minscope '$minscope' 22 --minscope '$minscope'
89 **What it does** 89 **What it does**
90 90
91 Compute small RNA (piRNA, siRNA, ...) signatures. 91 Compute small RNA (piRNA, siRNA, ...) signatures.
92 92
93 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores, 93 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores,
94 and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. 94 and (ii) the ping-pong signal (Brennecke et al. Science. 2008;322: 1387–1392) and associated z-scores.
95 95
96 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads 96 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads
97 when these reads can be aligned at multiple positions in the genome. The two values are equal only 97 when these reads can be aligned at multiple positions in the genome. The two values are equal only
98 when the analysis is restricted to uniquely mapping reads. 98 when the analysis is restricted to uniquely mapping reads.
99 99
100 Options set the min and max size of both the query small rna class and the target small rna class, 100 Options set the min and max size of both the query small rna class and the target small rna class,
101 the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at 101 the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at
102 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 102 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes
103 for piRNA and siRNA signatures, see `Antoniewski (2014)`_. 103 for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
104 104
105 .. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
106 .. _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
107 106
108 **Input** 107 **Input**
109 108
110 A **sorted** BAM alignment file. 109 A **sorted** BAM alignment file.