Mercurial > repos > earlhaminst > miranda

annotate miranda.xml @ 0:05bc31ccc323 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
author earlhaminst
date Fri, 11 Nov 2016 07:03:25 -0500
parents
children 89d595ffa9db
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
1 <tool id="miranda" name="miRanda" version="3.3a">
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
2 <description>finds potential target sites for miRNAs in genomic sequences</description>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
3 <requirements>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
4 <requirement type="package" version="3.3a">miranda</requirement>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
5 </requirements>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
6 <version_command>miranda --version|grep 'miranda v'</version_command>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
7 <command>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
8 <![CDATA[
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
9 miranda '$microrna' '$query'
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
10 #if str($sc)
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
11 -sc $sc
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
12 #end if
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
13 #if str($en)
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
14 -en $en
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
15 #end if
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
16 -out '$raw_output'
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
17 &&
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
18 python '$__tool_directory__/miranda_parser.py' '$raw_output' '$tabular_output'
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
19 ]]>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
20 </command>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
21 <inputs>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
22 <param name="microrna" type="data" format="fasta" label="MicroRNA sequences" help="FASTA format" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
23 <param name="query" type="data" format="fasta" label="Query sequences" help="FASTA format" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
24 <param name="sc" type="float" min="0.0" value="140.0" optional="true" label="Alignment score threshold" help="Only alignments with score greater or equal to this value will be used for further analysis (-sc)" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
25 <param name="en" type="float" value="1.0" optional="true" label="Set energy threshold to -E kcal/mol" help="Only alignments with energy less or equal to this value will be used for further analysis. A negative value is required for filtering to occur (-en)" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
26 </inputs>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
27 <outputs>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
28 <data name="raw_output" format="txt" label="${tool.name} on ${on_string}: raw output" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
29 <data name="tabular_output" format="tabular" label="${tool.name} on ${on_string}: tabular output" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
30 </outputs>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
31 <tests>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
32 <test>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
33 <param name="microrna" ftype="fasta" value="microrna.fasta" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
34 <param name="query" ftype="fasta" value="query.fasta" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
35 <output name="raw_output" file="raw_output.txt" lines_diff="4" />
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
36 </test>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
37 </tests>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
38 <help>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
39 <![CDATA[
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
40 `miRanda`_ is an algorithm for the detection of potential microRNA target sites in genomic sequences.
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
41
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
42 One or more miRNA sequences are scanned against all query sequences and potential target sites are reported. Potential target sites are identified using a two-step strategy. First a dynamic programming local alignment is carried out between the query miRNA sequence and the reference sequence. This alignment procedure scores based on sequence complementarity and not on sequence identity. In other words we look for A:U and G:C matches instead of A:A, G:G, etc. The G:U wobble bair is also permitted, but generally scores less than the more optimal matches.
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
43
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
44 The second phase of the algorithm takes high-scoring alignments (i.e. those above the alignment score threshold) detected from phase 1 and estimates the thermodynamic stability of RNA duplexes based on these alignments. This second phase of the method utilizes folding routines from the RNAlib library, which is part of the ViennaRNA package written by Ivo Hofacker. At this stage we generate a constrained fictional single-stranded RNA composed of the query sequence, a linker and the reference sequence (reversed). This structure is then folded using RNAlib and the minimum free energy (DG kcal/mol) is calculated for that structure.
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
45
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
46 Finally, detected targets with energies less than a chosen energy threshold are selected as potential target sites. Target site alignments passing both thresholds and other information is produced as output.
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
47
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
48 View the original miRanda manual: http://cbio.mskcc.org/microrna_data/manual.html
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
49
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
50 .. _miRanda: http://www.microrna.org/
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
51 ]]>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
52 </help>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
53 <citations>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
54 <citation type="doi">10.1186/gb-2003-5-1-r1</citation>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
55 </citations>
05bc31ccc323 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff changeset
56 </tool>