annotate TargetFinder.xml @ 0:773fdd1a02ea draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
author rnateam
date Wed, 21 Dec 2016 17:31:28 -0500
parents
children c9d56748fbde
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
1 <tool id="targetfinder" name="Plant small RNA target prediction tool" version="1.7.0">
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
2 <requirements>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
3 <requirement type="package" version="1.7">targetfinder</requirement>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
4 </requirements>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
5 <stdio>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
6 <exit_code range="1:" />
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
7 </stdio>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
8 <command><![CDATA[
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
9 targetfinder_threads.pl
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
10 -f $f
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
11 -d $d
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
12 -c $c
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
13 -t "\${GALAXY_SLOTS:-12}"
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
14 $r
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
15 -o $output1
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
16 ]]></command>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
17 <inputs>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
18 <param label="Input small RNA sequences file" help="(-f) FASTA-format" name="f" type="data" format="fasta" />
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
19 <param label="Target sequence database file" help="(-d) FASTA-format" name="d" type="data" format="fasta" />
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
20 <param label="Prediction score cutoff value" help="(-c) DEFAULT = 4" name="c" type="float" value="4.0" />
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
21 <param label="Search reverse strand for targets?" help="(-r) Use this option if the database is genomic DNA." name="r" type="boolean" falsevalue="" truevalue="-r" checked="false" />
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
22 </inputs>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
23 <outputs>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
24 <data name="output1" format="data"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
25 </outputs>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
26 <tests>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
27 <test>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
28 <param name="f" value="ath_miRNAs_test.fa"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
29 <param name="d" value="Antirrhinum_majus.mRNA.EST.fasta"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
30 <param name="r" value=""/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
31 <param name="c" value="4.0"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
32 <param name="t" value="1"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
33 <output name="output1" file="ath_miRNAs_predicted_targets.txt" compare="contains"/>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
34 </test>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
35 </tests>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
36 <help><![CDATA[
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
37 **What it does**
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
38
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
39 TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
40
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
41 This is done by aligning the input small RNA sequence against all transcripts,
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
42 followed by site scoring using a position-weighted scoring matrix.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
43
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
44 **Input**
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
45
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
46 -f Input small RNA sequences file (FASTA-format).
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
47
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
48 -d Target sequence database file (FASTA-format)
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
49
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
50 **Output**
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
51
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
52 Each predicted target site is printed out separately.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
53 The output consists of two parts.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
54
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
55 The first is a description line and the second is a base-pairing diagram of the target and small RNA (query) sequence.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
56
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
57 The description line contains the query name, the description line from the target sequence database, and the target prediction score.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
58
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
59 The base-pairing diagram has the target site sequence on top in 5'-3' orientation and the query sequence on the bottom in 3'-5' orientation.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
60
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
61 Between the target site sequece and the query sequence are base pair symbols.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
62
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
63 A ":" (colon) symbol represents an ordinary Watson-Crick base pair, a "." (period) represents a G:U base pair, and a " " (space) represents a mismatch.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
64
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
65 If a small RNA is predicted to target a sequence more than once, each target site will be output as separate output.
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
66 ]]></help>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
67 <citations>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
68 <citation type="doi">10.1016/j.cell.2005.04.004</citation>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
69 <citation type="doi">10.1371/journal.pone.0000219</citation>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
70 <citation type="doi">10.1007/978-1-60327-005-2_4</citation>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
71 </citations>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
72 </tool>
773fdd1a02ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
parents:
diff changeset
73