Mercurial > repos > artbio > small_rna_signatures
comparison signature.xml @ 14:5150d641d515 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
author | artbio |
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date | Thu, 06 Apr 2023 23:00:54 +0000 |
parents | 124f404b0fe7 |
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13:124f404b0fe7 | 14:5150d641d515 |
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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> |