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comparison spaln.xml @ 0:95ea8d97abb4 draft

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planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
author iuc
date Fri, 11 Jan 2019 18:15:21 -0500
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children 37b5e1f0b544
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-1:000000000000 0:95ea8d97abb4
1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.3.2</token>
5 </macros>
6 <edam_topics>
7 <edam_topic>topic_3512</edam_topic>
8 </edam_topics>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
11 </requirements>
12 <command detect_errors="aggressive"><![CDATA[
13 spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query'
14 ]]></command>
15 <inputs>
16 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
17 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
18 <param argument="-O" type="select" name="format" label="Output format">
19 <option value="0">GFF3 format genes</option>
20 <option value="2">GFF3 format matches</option>
21 <option value="3">BED format</option>
22 <option value="4">Tabular format exon information</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="output1" format="tabular">
27 <change_format>
28 <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
29 <when input="format" value="0" format="gff3" />
30 <when input="format" value="2" format="gff3" />
31 <when input="format" value="3" format="bed12" />
32 <when input="format" value="4" format="tabular" />
33 </change_format>
34 <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
35 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
36 commented out till that is merged
37 <actions>
38 <conditional name="format">
39 <when value="4">
40 <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T # - X P DiNuc" />
41 </when>
42 </conditional>
43 </actions>
44 -->
45 </data>
46 </outputs>
47 <tests>
48 <test>
49 <param name="genome" ftype="fasta" value="genome.fasta" />
50 <param name="query" ftype="fasta" value="query.fasta" />
51 <param name="format" value="0"/>
52 <output name="output1" value="output1_gff_genes.gff3" />
53 </test>
54 <test>
55 <param name="genome" ftype="fasta" value="genome.fasta" />
56 <param name="query" ftype="fasta" value="query.fasta" />
57 <param name="format" value="2"/>
58 <output name="output1" value="output1_gff_matches.gff3" />
59 </test>
60 <test>
61 <param name="genome" ftype="fasta" value="genome.fasta" />
62 <param name="query" ftype="fasta" value="query.fasta" />
63 <param name="format" value="3"/>
64 <output name="output1" value="output1.bed12" />
65 </test>
66 <test>
67 <param name="genome" ftype="fasta" value="genome.fasta" />
68 <param name="query" ftype="fasta" value="query.fasta" />
69 <param name="format" value="4"/>
70 <output name="output1" value="output1.tabular" />
71 </test>
72 </tests>
73 <help><![CDATA[
74 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
75 protein sequences onto a whole genomic sequence in a single job.
76
77 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters.
78
79 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
80 ]]></help>
81 <citations>
82 <citation type="doi">0.1093/nar/gkn105</citation>
83 </citations>
84 </tool>