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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
author artbio
date Thu, 06 Apr 2023 23:00:54 +0000
parents 124f404b0fe7
children
comparison
equal deleted inserted replaced
13:124f404b0fe7 14:5150d641d515
1 <tool id="signature" name="Small RNA Signatures" version="3.4.2>"> 1 <tool id="signature" name="Small RNA Signatures" version="3.5.0">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.23.4">numpy</requirement> 4 <requirement type="package" version="1.23.4">numpy</requirement>
5 <requirement type="package" version="0.18.0">pysam</requirement> 5 <requirement type="package" version="0.18.0">pysam</requirement>
6 <requirement type="package" version="1.7.3">r-optparse</requirement> 6 <requirement type="package" version="1.7.3">r-optparse</requirement>
24 --output_h '$h_dataframe' 24 --output_h '$h_dataframe'
25 --output_z '$z_dataframe' && 25 --output_z '$z_dataframe' &&
26 Rscript '$__tool_directory__'/signature.r 26 Rscript '$__tool_directory__'/signature.r
27 --h_dataframe '$h_dataframe' 27 --h_dataframe '$h_dataframe'
28 --z_dataframe '$z_dataframe' 28 --z_dataframe '$z_dataframe'
29 --plot_method '$plot_method' 29 --plot_method '$plot_options.plot_method'
30 --pdf '$pdf' 30 --pdf '$pdf'
31 --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs" 31 --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
32 #if $plot_options.plot_method == "global":
33 --npairs_ylim $plot_options.npairs_ylim
34 --npairszscore_ylim $plot_options.npairszscore_ylim
35 --overlapprob_ylim $plot_options.overlapprob_ylim
36 --overlapprobzscore_ylim $plot_options.overlapprobzscore_ylim
37 #end if
32 ]]></command> 38 ]]></command>
33 <inputs> 39 <inputs>
34 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> 40 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
35 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> 41 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
36 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> 42 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
37 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> 43 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
38 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> 44 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
39 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" /> 45 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
40 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" /> 46 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
41 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select"> 47 <conditional name="plot_options">
42 <option selected="True" value="global">Global</option> 48 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
43 <option value="lattice">Lattice</option> 49 <option selected="True" value="global">Global</option>
44 </param> 50 <option value="lattice">Lattice</option>
51 </param>
52 <when value="lattice" />
53 <when value="global">
54 <param name="npairs_ylim" type="integer" value="0" optional="true"
55 label="Maximum of Y-scale of the Numbers-of-pairs plot"
56 help="Interger. Leave 0 for self-determination of Y-scale" />
57 <param name="npairszscore_ylim" type="integer" value="0" optional="true"
58 label="Maximum of Y-scale of the Number-of-pairs-Z−scores plot"
59 help="Integer. Leave 0 for self-determination of Y-scale" />
60 <param name="overlapprob_ylim" type="integer" value="0" optional="true"
61 label="Maximum of Y-scale of the Overlap-probabilities plot"
62 help="Percent value as an Integer. Leave 0 for self-determination of % Y-scale" />
63 <param name="overlapprobzscore_ylim" type="integer" value="0" optional="true"
64 label="Maximum of Y-scale of the Overlap-probabilities-Z−scores plot"
65 help="Interger. Leave 0 for self-determination of Y-scale" />
66 </when>
67 </conditional>
45 </inputs> 68 </inputs>
46 <outputs> 69 <outputs>
47 <data format="tabular" label="z-signature data frame" name="z_dataframe"> 70 <data format="tabular" label="z-signature data frame" name="z_dataframe">
48 <actions> 71 <actions>
49 <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" /> 72 <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />
63 <param name="maxquery" value="29" /> 86 <param name="maxquery" value="29" />
64 <param name="mintarget" value="23" /> 87 <param name="mintarget" value="23" />
65 <param name="maxtarget" value="29" /> 88 <param name="maxtarget" value="29" />
66 <param name="minscope" value="5" /> 89 <param name="minscope" value="5" />
67 <param name="maxscope" value="15" /> 90 <param name="maxscope" value="15" />
68 <param name="plot_method" value="global" /> 91 <conditional name="plot_options">
92 <param name="plot_method" value="global" />
93 </conditional>
69 <output file="h.tab" ftype="tabular" name="h_dataframe" /> 94 <output file="h.tab" ftype="tabular" name="h_dataframe" />
70 <output file="z.tab" ftype="tabular" name="z_dataframe" /> 95 <output file="z.tab" ftype="tabular" name="z_dataframe" />
71 <output file="global.pdf" ftype="pdf" name="pdf" /> 96 <output file="global.pdf" ftype="pdf" name="pdf" />
72 </test> 97 </test>
98
73 <test> 99 <test>
74 <param ftype="bam" name="input" value="sr_bowtie.bam" /> 100 <param ftype="bam" name="input" value="sr_bowtie.bam" />
75 <param name="minquery" value="23" /> 101 <param name="minquery" value="23" />
76 <param name="maxquery" value="29" /> 102 <param name="maxquery" value="29" />
77 <param name="mintarget" value="23" /> 103 <param name="mintarget" value="23" />
78 <param name="maxtarget" value="29" /> 104 <param name="maxtarget" value="29" />
79 <param name="minscope" value="5" /> 105 <param name="minscope" value="5" />
80 <param name="maxscope" value="15" /> 106 <param name="maxscope" value="15" />
81 <param name="plot_method" value="lattice" /> 107 <conditional name="plot_options">
108 <param name="plot_method" value="global" />
109 </conditional>
110 <param name="npairs_ylim" value="100" />
111 <param name="npairszscore_ylim" value="0" />
112 <param name="overlapprob_ylim" value="1" />
113 <param name="overlapprobzscore_ylim" value="4" />
114
115 <output file="h.tab" ftype="tabular" name="h_dataframe" />
116 <output file="z.tab" ftype="tabular" name="z_dataframe" />
117 <output file="global-limited.pdf" ftype="pdf" name="pdf" />
118 </test>
119
120 <test>
121 <param ftype="bam" name="input" value="sr_bowtie.bam" />
122 <param name="minquery" value="23" />
123 <param name="maxquery" value="29" />
124 <param name="mintarget" value="23" />
125 <param name="maxtarget" value="29" />
126 <param name="minscope" value="5" />
127 <param name="maxscope" value="15" />
128 <conditional name="plot_options">
129 <param name="plot_method" value="lattice" />
130 </conditional>
82 <output file="h.tab" ftype="tabular" name="h_dataframe" /> 131 <output file="h.tab" ftype="tabular" name="h_dataframe" />
83 <output file="z.tab" ftype="tabular" name="z_dataframe" /> 132 <output file="z.tab" ftype="tabular" name="z_dataframe" />
84 <output file="lattice.pdf" ftype="pdf" name="pdf" /> 133 <output file="lattice.pdf" ftype="pdf" name="pdf" />
85 </test> 134 </test>
86 </tests> 135 </tests>