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annotate 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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aa5e2c64dff8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
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1 <tool id="signature" name="Small RNA Signatures" version="3.4.1>">
0
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2 <description />
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3 <requirements>
12
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4 <requirement type="package" version="1.23.4">numpy</requirement>
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5 <requirement type="package" version="0.18.0">pysam</requirement>
aa5e2c64dff8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
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6 <requirement type="package" version="1.7.3">r-optparse</requirement>
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7 <requirement type="package" version="0.6_30">r-latticeextra</requirement>
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8 <requirement type="package" version="2.3">r-gridextra</requirement>
0
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Tool exception" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
12
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14 ln -f -s $input.metadata.bam_index input.bam.bai &&
aa5e2c64dff8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
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15 ln -s $input input.bam &&
0
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16 python '$__tool_directory__'/signature.py
12
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17 --input input.bam
0
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18 --minquery '$minquery'
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19 --maxquery '$maxquery'
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20 --mintarget '$mintarget'
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21 --maxtarget '$maxtarget'
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22 --minscope '$minscope'
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23 --maxscope '$maxscope'
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24 --output_h '$h_dataframe'
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25 --output_z '$z_dataframe' &&
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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26 Rscript '$__tool_directory__'/signature.r
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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27 --h_dataframe '$h_dataframe'
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28 --z_dataframe '$z_dataframe'
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29 --plot_method '$plot_method'
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30 --pdf '$pdf'
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31 --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
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32 ]]></command>
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33 <inputs>
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34 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
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35 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
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36 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
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37 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
a35e6f9c1d34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8
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38 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
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39 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
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40 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
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41 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
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42 <option selected="True" value="global">Global</option>
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43 <option value="lattice">Lattice</option>
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" label="z-signature data frame" name="z_dataframe">
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48 <actions>
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49 <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />
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50 </actions>
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51 </data>
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52 <data format="tabular" label="h-signature data frame" name="h_dataframe">
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53 <actions>
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54 <action name="column_names" type="metadata" default="Chromosome,Overlap,overlap_probability,z-score" />
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55 </actions>
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56 </data>
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57 <data format="pdf" label="Overlap probabilities" name="pdf" />
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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62 <param name="minquery" value="23" />
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63 <param name="maxquery" value="29" />
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64 <param name="mintarget" value="23" />
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65 <param name="maxtarget" value="29" />
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66 <param name="minscope" value="5" />
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67 <param name="maxscope" value="15" />
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68 <param name="plot_method" value="global" />
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69 <output file="h.tab" ftype="tabular" name="h_dataframe" />
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70 <output file="z.tab" ftype="tabular" name="z_dataframe" />
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71 <output file="global.pdf" ftype="pdf" name="pdf" />
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72 </test>
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73 <test>
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74 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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75 <param name="minquery" value="23" />
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76 <param name="maxquery" value="29" />
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77 <param name="mintarget" value="23" />
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78 <param name="maxtarget" value="29" />
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79 <param name="minscope" value="5" />
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80 <param name="maxscope" value="15" />
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81 <param name="plot_method" value="lattice" />
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82 <output file="h.tab" ftype="tabular" name="h_dataframe" />
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83 <output file="z.tab" ftype="tabular" name="z_dataframe" />
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84 <output file="lattice.pdf" ftype="pdf" name="pdf" />
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85 </test>
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86 </tests>
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87 <help>
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88
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89 **What it does**
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90
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91 Compute small RNA (piRNA, siRNA, ...) signatures.
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92
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93 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores,
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94 and (ii) the ping-pong signal (Brennecke et al. Science. 2008;322: 1387–1392) and associated z-scores.
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95
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96 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads
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97 when these reads can be aligned at multiple positions in the genome. The two values are equal only
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98 when the analysis is restricted to uniquely mapping reads.
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99
0
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100 Options set the min and max size of both the query small rna class and the target small rna class,
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101 the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at
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102 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes
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103 for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
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104
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105 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
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106
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107 **Input**
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108
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109 A **sorted** BAM alignment file.
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110
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111 **Outputs**
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112
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113 **Global**: The number of pairs found, the ping-pong signal and the associated z-scores
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114 are computed at genome-wide level and returned in a pdf file.
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115
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116 **Lattice**: The number of pairs found, the ping-pong signals and the associated z-scores
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117 are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.
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118
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119
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
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123 </citations>
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124 </tool>