annotate egglib/CalculateDiversityIndexes.xml @ 6:ebb0ac9b6fa9 draft

planemo upload

1 <tool id="calculate_diversity" name="Diversity by gene" version="2.1.6">
2 	<description>calculates various diversity indexes with EggLib.</description>
3     <!-- [STRONGLY RECOMMANDED] Exit code rules -->
4     <stdio>
5         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
6         <exit_code range="1:" level="fatal" />
7     </stdio>
8     <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log
9     </command>
10 	<inputs>
11 		<param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/>
12 	</inputs>
13 	<outputs>
14 		<data format="txt" name="output" label="Diversity"/>
15 		<data format="txt" name="log" label="Logfile"/>
16 	</outputs>
17     
18     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
19     <tests>
20         <!-- [HELP] Test files have to be in the ~/test-data directory -->
21         <!-- [HELP] Multiple tests can be defined with different parameters -->
22         <test>
23          <param name="input" value="egglib-alignment.fa" />
24          <output name="output" file="egglib-result.txt" />
25         </test>
26     </tests>
27 	<help>
28 	
29 
30 
31 .. class:: infomark
32 
33 **Authors** EggLib_
34 
35 .. _EggLib: http://egglib.sourceforge.net/
36 
37   | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27.
38 
39 .. class:: infomark
40 
41 **Galaxy integration** South Green.
42 
43 .. class:: infomark
44 
45 **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
46 
47 ---------------------------------------------------
48 
49 
50 
51 ==================
52 Diversity by genes
53 ==================
54 
55 -----------
56 Description
57 -----------
58 
59   | Provides various diversity indexes using EggLib library.
60   | For further informations, please visite the EggLib website_.
61 
62 .. _website: http://egglib.sourceforge.net/
63 
64 
65 -----------------
66 Workflow position
67 -----------------
68 
69 **Upstream tool**
70 
71 =============== ====================== ===========
72 Name            output file(s)         format 
73 =============== ====================== ===========
74 VCF to Hapmap   Fasta alignment        fasta
75 =============== ====================== ===========
76 
77 
78 
79 ----------
80 Input file
81 ----------
82 
83 Fasta file
84 	Fasta alignment
85 
86 
87 
88 ------------
89 Output files
90 ------------
91 
92 Diversity
93 
94 Log file
95 
96 
97 ------------
98 Dependencies
99 ------------
00 EggLib 
01 	version 2.1.5
02 
03 ---------------------------------------------------
04 
05 ---------------
06 Working example
07 ---------------
08 
09 Input files
10 ===========
11 
12 Fasta file
13 ----------
14 
15 ::
16 	
17 	>LOCOs11g09160_AZUCENA_1
18 	ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
19 	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
20 	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
21 	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
22 	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
23 	>LOCOs11g09160_AZUCENA_2
24 	ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
25 	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
26 	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
27 	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
28 	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
29 	>LOCOs11g09160_BULUPANDAK_1
30 	ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
31 	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
32 	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
33 	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
34 	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
35 	>LOCOs11g09160_BULUPANDAK_2
36 	ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
37 	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
38 	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
39 	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
40 	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
41 	>LOCOs07g23169_AZUCENA_1
42 	ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA
43 	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
44 	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
45 
46 Output files
47 ============
48 
49 Diversity
50 ---------
51 
52 ::
53 
54 	LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1;
55 	LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1;
56 
57 
58 	</help>
59     <citations>
60         <!-- [HELP] As DOI or BibTex entry -->
61     	<citation type="bibtex">@article{Dereeper03062015,
62 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
63 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
64 year = {2015}, 
65 doi = {10.1093/nar/gkv351}, 
66 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
67 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
68 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
69 journal = {Nucleic Acids Research} 
70 }
71 
72     	</citation>
73 
74     </citations>
75 </tool>