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comparison pipelign.xml @ 0:cd9d1eccda7e draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
author iuc
date Fri, 23 Aug 2019 14:47:13 -0400
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-1:000000000000 0:cd9d1eccda7e
1 <?xml version="1.0"?>
2 <tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0">
3 <description>alignment with pipelign</description>
4 <macros>
5 <token name="@VERSION@">0.2</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@VERSION@">pipelign</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 pipelign
12 --outDir files
13 --clearExistingDirectory
14 --inFile '$inFile'
15 --outFile '$outFile'
16 --lenThr $lenThr
17 --alphabet $alphabet
18 --simPer $simPer
19 --merge $merge
20 --thread \${GALAXY_SLOTS:-1}
21 --mIterateLong $mIterateLong
22 --mIterateMerge $mIterateMerge
23 --ambigPer $ambigPer
24 $keepOrphans $keepBadSeqs $excludeClusters
25 ]]></command>
26 <inputs>
27 <param argument="--inFile" type="data" format="fasta" label="Input sequence file" />
28 <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" />
29 <param argument="--alphabet" type="select" label="Alphabet for input sequences">
30 <option value="dna">DNA</option>
31 <option value="rna">RNA</option>
32 <option value="aa">Amino Acids</option>
33 </param>
34 <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" />
35 <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" />
36 <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" />
37 <param argument="--merge" type="select" label="Merge strategy">
38 <option value="P">Parallel</option>
39 <option value="C">Consensus</option>
40 </param>
41 <param argument="--mIterateLong" type="integer" value="1" min="1" label="Number of iterations to refine long alignments" />
42 <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" />
43 <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" />
44 <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" />
45 </inputs>
46 <outputs>
47 <data name="outFile" format="fasta" />
48 </outputs>
49 <tests>
50 <test>
51 <param name="inFile" value="pipelign-in1.fasta" />
52 <output name="outFile">
53 <assert_contents>
54 <has_line line="&gt;K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" />
55 <has_line line="&gt;K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" />
56 <has_line line="&gt;K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" />
57 <has_line line="&gt;K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" />
58 <has_line line="&gt;K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" />
59 <has_line line="&gt;K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" />
60 <has_line line="&gt;K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" />
61 <has_line line="&gt;K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" />
62 </assert_contents>
63 </output>
64 </test>
65 </tests>
66 <help><![CDATA[
67 .. class:: infomark
68
69 **What it does**
70
71 -------------------
72
73 A pipeline for automated multiple sequence alignment, particularly of viral sequences.
74
75 ]]>
76 </help>
77 <citations>
78 <citation type="bibtex">
79 @UNPUBLISHED{spond,
80 author = "A.S.Md.M. Hossain, S.D.W.Frost",
81 title = "Pipelign: an alignment pipeline for viral sequences.",
82 year = "2019",
83 note = "https://github.com/asmmhossain/pipelign/",
84 url = "https://github.com/asmmhossain/pipelign/"}
85 </citation>
86 </citations>
87 </tool>