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comparison signature.xml @ 2:2b30861d95f4 draft

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author mvdbeek
date Sun, 29 Mar 2015 11:58:31 -0400
parents 9274c7b1e85c
children 741cc1d16813
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1:9274c7b1e85c 2:2b30861d95f4
1 <tool id="signature" name="Small RNA Signatures" version="2.0.1"> 1 <tool id="signature" name="Small RNA Signatures" version="2.0.1">
2 <description></description> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 6 <requirement type="package" version="0.7.7">pysam</requirement>
7 <requirement type="package" version="2.14">biocbasics</requirement> 7 <requirement type="package" version="2.14">biocbasics</requirement>
8 <requirement type="package" version="3.0.3">R</requirement> 8 <requirement type="package" version="3.0.3">R</requirement>
9 </requirements> 9 <requirement type="package" version="1.9">numpy</requirement>
10 <command interpreter="python"> 10 <requirement type="package" version="0.14">scipy</requirement>
11 </requirements>
12 <command interpreter="python">
11 signature.py 13 signature.py
12 --input $refGenomeSource.input 14 --input $refGenomeSource.input
13 --inputFormat $refGenomeSource.input.ext 15 --inputFormat $refGenomeSource.input.ext
14 --minquery $minquery 16 --minquery $minquery
15 --maxquery $maxquery 17 --maxquery $maxquery
26 --extract_index 28 --extract_index
27 #end if 29 #end if
28 --graph $graph_type 30 --graph $graph_type
29 --rcode $sigplotter 31 --rcode $sigplotter
30 </command> 32 </command>
33 <inputs>
34 <conditional name="refGenomeSource">
35 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
36 <option value="indexed">Use a built-in index</option>
37 <option value="history">Use one from the history</option>
38 </param>
39 <when value="indexed">
40 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data">
41 <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" />
42 </param>
43 </when>
44 <when value="history">
45 <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" />
46 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
47 </when>
48 </conditional>
49 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
50 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
51 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
52 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
53 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
54 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
55 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select">
56 <option selected="True" value="global">Global</option>
57 <option value="lattice">Lattice</option>
58 </param>
59 </inputs>
60 <outputs>
61 <data format="tabular" label="signature data frame" name="output" />
62 <data format="pdf" label="Overlap probabilities" name="output2" />
63 </outputs>
64 <tests>
65 <test>
66 <param name="genomeSource" value="history" />
67 <param ftype="fasta" name="ownFile" value="ensembl.fa" />
68 <param ftype="bam" name="input" value="sr_bowtie.bam" />
69 <param name="minquery" value="23" />
70 <param name="maxquery" value="29" />
71 <param name="mintarget" value="23" />
72 <param name="maxtarget" value="29" />
73 <param name="minscope" value="5" />
74 <param name="maxscope" value="15" />
75 <param name="graph_type" value="global" />
76 <output file="signature.tab" ftype="tabular" name="output" />
77 <output file="signature.pdf" ftype="pdf" name="output2" />
78 </test>
79 </tests>
80 <help>
31 81
32 <inputs> 82 **What it does**
33 <conditional name="refGenomeSource">
34 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
35 <option value="indexed">Use a built-in index</option>
36 <option value="history">Use one from the history</option>
37 </param>
38 <when value="indexed">
39 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output">
40 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
41 </param>
42 </when>
43 <when value="history">
44 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
45 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output"/>
46 </when>
47 </conditional> <!-- refGenomeSource -->
48 <param name="minquery" type="integer" size="3" value="23" label="Min size of query small RNAs" help="'23' = 23 nucleotides"/>
49 <param name="maxquery" type="integer" size="3" value="29" label="Max size of query small RNAs" help="'29' = 29 nucleotides"/>
50 <param name="mintarget" type="integer" size="3" value="23" label="Min size of target small RNAs" help="'23' = 23 nucleotides"/>
51 <param name="maxtarget" type="integer" size="3" value="29" label="Max size of target small RNAs" help="'29' = 29 nucleotides"/>
52 <param name="minscope" type="integer" size="3" value="1" label="Minimal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
53 <param name="maxscope" type="integer" size="3" value="26" label="Maximal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
54 <param name="graph_type" type="select" label="Graph type" help="Signature can be computed globally or by item present in the alignment file">
55 <option value="global" selected="True">Global</option>
56 <option value="lattice">Lattice</option>
57 </param>
58 </inputs>
59 83
60 <configfiles> 84 This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
61 <configfile name="sigplotter"> 85 The numerical options set the min and max size of both the query small rna class and the target small rna class.
86 Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
87
88 </help>
89 <citations>
90 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
91 </citations>
92 <configfiles>
93 <configfile name="sigplotter">
62 graph_type = "${graph_type}" 94 graph_type = "${graph_type}"
63 95
64 globalgraph = function () { 96 globalgraph = function () {
65 ## Setup R error handling to go to stderr 97 ## Setup R error handling to go to stderr
66 options( show.error.messages=F, 98 options( show.error.messages=F,
110 } 142 }
111 if(graph_type=="lattice") { 143 if(graph_type=="lattice") {
112 treillisgraph() 144 treillisgraph()
113 } 145 }
114 </configfile> 146 </configfile>
115 </configfiles> 147 </configfiles>
116
117 <outputs>
118 <data name="output" format="tabular" label = "signature data frame"/>
119 <data name="output2" format="pdf" label="Overlap probabilities"/>
120 </outputs>
121
122 <help>
123
124 **What it does**
125
126 This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
127 The numerical options set the min and max size of both the query small rna class and the target small rna class
128 Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
129
130 </help>
131
132 <tests>
133 <test>
134 <param name="genomeSource" value="history" />
135 <param name="ownFile" value ="ensembl.fa" ftype="fasta" />
136 <param name="input" value="sr_bowtie.bam" ftype="bam" />
137 <param name="minquery" value="23" />
138 <param name="maxquery" value="29" />
139 <param name="mintarget" value="23" />
140 <param name="maxtarget" value="29" />
141 <param name="minscope" value="5" />
142 <param name="maxscope" value="15" />
143 <param name="graph_type" value="global" />
144 <output name="output" ftype="tabular" file="signature.tab"/>
145 <output name="output2" ftype="pdf" file="signature.pdf"/>
146 </test>
147 </tests>
148
149
150 </tool> 148 </tool>
151