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comparison GAFA.xml @ 1:fc8ca4ade638 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 81a1e79dda127d1afc16c7e456bbec16093a3c3f-dirty
author earlhaminst
date Mon, 20 Feb 2017 06:25:33 -0500
parents af9f72ddf7f9
children 117fc7414307
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0:af9f72ddf7f9 1:fc8ca4ade638
1 <tool id="gafa" name="Gene Align and Family Aggregator" version="0.1.0"> 1 <tool id="gafa" name="Gene Align and Family Aggregator" version="0.2.0">
2 <description>generates an SQLite database that can be visualised with Aequatus</description> 2 <description>generates an SQLite database that can be visualised with Aequatus</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 python '$__tool_directory__/GAFA.py' 5 python '$__tool_directory__/GAFA.py'
6 #for $dataset in $treeFile: 6 #for $dataset in $treeFile:
7 -t '$dataset' 7 -t '$dataset'
8 #end for 8 #end for
9 #for $dataset in $alignmentFile: 9 #for $dataset in $alignmentFile:
10 -c '$dataset' 10 -a '$dataset'
11 #end for 11 #end for
12 -g '$genesFile' 12 -g '$genesFile'
13 -o '$outputFile' 13 -o '$outputFile'
14 ]]> 14 ]]>
15 </command> 15 </command>
16 <inputs> 16 <inputs>
17 <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" /> 17 <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
18 <param name="alignmentFile" type="data" format="tabular" multiple="true" label="CDS alignments" help="CDS alignments in tabular format generated by 'T-Coffee to CIGAR' tool" /> 18 <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
19 <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get Ensembl features by ID' tool" /> 19 <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get features by Ensembl ID' tool" />
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" /> 22 <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="treeFile" ftype="nhx" value="tree.nhx" /> 26 <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" />
27 <param name="alignmentFile" ftype="tabular" value="cigar.tabular" /> 27 <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" />
28 <param name="genesFile" ftype="json" value="gene.json" /> 28 <param name="genesFile" ftype="json" value="gene.json" />
29 <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" /> 29 <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
30 </test> 30 </test>
31 </tests> 31 </tests>
32 <help> 32 <help>
33 <![CDATA[ 33 <![CDATA[
34 Simple tool to generate an SQLite database that can be visualised with `Aequatus`_. 34 Simple tool to generate an SQLite database that can be visualised with `Aequatus`_.
35 35
36 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures. 36 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.
37 37
38 N.B.: The tool will modify the sequence identifiers found in the "CDS alignments" dataset by removing everything from the first underscore to the end of the string. 38 N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string.
39 39
40 .. _Aequatus: http://aequatus.earlham.ac.uk 40 .. _Aequatus: http://aequatus.earlham.ac.uk
41 ]]> 41 ]]>
42 </help> 42 </help>
43 <citations> 43 <citations>