Mercurial > repos > drosofff > msp_sr_signature
annotate signature.xml @ 5:837e4350661f draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 2588072aa6ffd90f0c8b63c61222bd817af7c76a
author | drosofff |
---|---|
date | Thu, 21 Dec 2017 08:54:03 -0500 |
parents | e77c0b28e9a2 |
children |
rev | line source |
---|---|
5
837e4350661f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 2588072aa6ffd90f0c8b63c61222bd817af7c76a
drosofff
parents:
4
diff
changeset
|
1 <tool id="signature" name="Small RNA Signatures" version="2.1.2.1"> |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
2 <description /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
3 <requirements> |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
4 <requirement type="package" version="1.1.2">bowtie</requirement> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
5
837e4350661f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 2588072aa6ffd90f0c8b63c61222bd817af7c76a
drosofff
parents:
4
diff
changeset
|
7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement> |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
8 </requirements> |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
9 <command><![CDATA[ |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
10 python '$__tool_directory__'/signature.py |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
11 --input '$refGenomeSource.input' |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
12 --inputFormat '$refGenomeSource.input.ext' |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
13 --minquery $minquery |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
14 --maxquery $maxquery |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
15 --mintarget $mintarget |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
16 --maxtarget $maxtarget |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
17 --minscope $minscope |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
18 --maxscope $maxscope |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
19 --outputOverlapDataframe $output |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
20 #if $refGenomeSource.genomeSource == "history": |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
21 --referenceGenome '$refGenomeSource.ownFile' |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
22 #else: |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
23 #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
24 --referenceGenome '$reference' |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
25 --extract_index |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
26 #end if |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
27 --graph $graph_type |
1
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
28 --rcode '$sigplotter' |
6218b518cd16
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
0
diff
changeset
|
29 ]]></command> |
0
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
30 <inputs> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
31 <conditional name="refGenomeSource"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
32 <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"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
33 <option value="indexed">Use a built-in index</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
34 <option value="history">Use one from the history</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
35 </param> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
36 <when value="indexed"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
37 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
38 <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" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
39 </param> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
40 </when> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
41 <when value="history"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
42 <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
43 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
44 </when> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
45 </conditional> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
46 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
47 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
48 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
49 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
50 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
51 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
52 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
53 <option selected="True" value="global">Global</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
54 <option value="lattice">Lattice</option> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
55 </param> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
56 </inputs> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
57 <outputs> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
58 <data format="tabular" label="signature data frame" name="output" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
59 <data format="pdf" label="Overlap probabilities" name="output2" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
60 </outputs> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
61 <tests> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
62 <test> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
63 <param name="genomeSource" value="history" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
64 <param ftype="fasta" name="ownFile" value="ensembl.fa" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
65 <param ftype="bam" name="input" value="sr_bowtie.bam" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
66 <param name="minquery" value="23" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
67 <param name="maxquery" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
68 <param name="mintarget" value="23" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
69 <param name="maxtarget" value="29" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
70 <param name="minscope" value="5" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
71 <param name="maxscope" value="15" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
72 <param name="graph_type" value="global" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
73 <output file="signature.tab" ftype="tabular" name="output" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
74 <output file="signature.pdf" ftype="pdf" name="output2" /> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
75 </test> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
76 </tests> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
77 <help> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
78 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
79 **What it does** |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
80 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
81 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. |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
82 The numerical options set the min and max size of both the query small rna class and the target small rna class. |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
83 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. |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
84 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
85 </help> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
86 <citations> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
87 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
88 </citations> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
89 <configfiles> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
90 <configfile name="sigplotter"> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
91 graph_type = "${graph_type}" |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
92 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
93 globalgraph = function () { |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
94 ## Setup R error handling to go to stderr |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
95 options( show.error.messages=F, |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
96 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
97 signature = read.delim("${output}", header=TRUE) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
98 signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2])) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
99 overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3])) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
100 YLIM=max(signature[,2]) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
101 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
102 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
103 ## Open output2 PDF file |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
104 pdf( "${output2}" ) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
105 if (YLIM!=0) { |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
106 par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
107 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
108 plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
109 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
110 plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
111 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
112 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities", |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
113 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50), |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
114 pch=19, col="darkslateblue", lwd=2) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
115 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
116 plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
117 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
118 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
119 } |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
120 devname = dev.off() |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
121 ## Close the PDF file |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
122 } |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
123 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
124 treillisgraph = function () { |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
125 ## Open output2 PDF file |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
126 pdf( "${output2}", paper="special", height=11.69, width=8.2677 ) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
127 signature = read.delim("${output}", header=TRUE) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
128 options( show.error.messages=F, |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
129 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
130 library(lattice) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
131 print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(${minscope},${maxscope}), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
132 par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5), |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
133 cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]", |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
134 pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2, |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
135 layout=c(4,12), as.table=TRUE, newpage = T) ) |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
136 devnname = dev.off() |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
137 } |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
138 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
139 if (graph_type=="global") { |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
140 globalgraph() |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
141 |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
142 } |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
143 if(graph_type=="lattice") { |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
144 treillisgraph() |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
145 } |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
146 </configfile> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
147 </configfiles> |
a2f293717ce3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff
changeset
|
148 </tool> |