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comparison dereplication.xml @ 1:8c4e2933a17a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
author iuc
date Wed, 26 Aug 2015 13:34:22 -0400
parents fae6527990af
children f29e21388219
comparison
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0:fae6527990af 1:8c4e2933a17a
1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.0"> 1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
16 #end if 16 #end if
17 #if $minuniquesize: 17 #if $minuniquesize:
18 --minuniquesize $minuniquesize 18 --minuniquesize $minuniquesize
19 #end if 19 #end if
20 --output $outfile 20 --output $outfile
21 #if $sizein: 21 $sizein
22 --sizein $sizein 22 $sizeout
23 --strand $strand
24 #if $topn:
25 --topn $topn
23 #end if 26 #end if
24 #if $sizeout:
25 --sizeout $sizeout
26 #end if
27 --strand $strand
28 --topn $topn
29 #if $uc: 27 #if $uc:
30 --uc $uc 28 --uc $uc_outfile
31 #end if 29 #end if
32 ]]> 30 ]]>
33 </command> 31 </command>
34 <inputs> 32 <inputs>
35 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" /> 33 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" />
43 <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance" 41 <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance"
44 help="(--maxuniquesize)"/> 42 help="(--maxuniquesize)"/>
45 </inputs> 43 </inputs>
46 <outputs> 44 <outputs>
47 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> 45 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
48 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> 46 <data name="uc_outfile" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
49 <filter>uc is True</filter> 47 <filter>uc is True</filter>
50 </data> 48 </data>
51 </outputs> 49 </outputs>
52 <tests> 50 <tests>
53 <test> 51 <test>
54 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" /> 52 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
55 <param name="strand" value="both" /> 53 <param name="strand" value="both" />
56 <param name="minuniquesize" value="1" /> 54 <param name="minuniquesize" value="1" />
57 <param name="maxuniquesize" value="100000" /> 55 <param name="maxuniquesize" value="100000" />
56 <param name="topn" value="10000" />
57 <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
58 </test>
59 <test>
60 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
61 <param name="strand" value="both" />
62 <param name="minuniquesize" value="1" />
63 <param name="maxuniquesize" value="100000" />
64 <param name="sizeout" value="--sizeout"/>
65 <param name="topn" value="" />
66 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
67 </test>
68 <test>
69 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
70 <param name="strand" value="both" />
71 <param name="minuniquesize" value="1" />
72 <param name="maxuniquesize" value="100000" />
58 <param name="sizeout" value="--sizeout"/> 73 <param name="sizeout" value="--sizeout"/>
59 <param name="topn" value="10000" /> 74 <param name="topn" value="10000" />
60 <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" /> 75 <param name="uc" value="--uc" />
76 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
77 <output name="uc_outfile" file="dereplication_uc_result3.fasta" ftype="fasta" />
61 </test> 78 </test>
62 </tests> 79 </tests>
63 <help> 80 <help>
64 <![CDATA[ 81 <![CDATA[
65 **What it does** 82 **What it does**