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comparison sorting.xml @ 0:24e4f42410e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
author iuc
date Mon, 11 May 2015 22:46:54 -0400
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-1:000000000000 0:24e4f42410e5
1 <tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0">
2 <description></description>
3 <macros>
4 <import>vsearch_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command>
10 <![CDATA[
11 vsearch
12 @GENERAL@
13 #if $sorting_mode.sorting_mode_select == 'sortbylength':
14 --sortbylength "$sorting_mode.infile"
15 #else:
16 --sortbysize "$sorting_mode.infile"
17 #if $sorting_mode.minsize:
18 --minsize $sorting_mode.minsize
19 #end if
20 #if $sorting_mode.maxsize:
21 --maxsize $sorting_mode.maxsize
22 #end if
23 #end if
24 --output $outfile
25 #if $sizeout:
26 --sizeout $sizeout
27 #end if
28 #if $topn:
29 --topn $topn
30 #end if
31
32 ]]>
33 </command>
34 <inputs>
35 <conditional name="sorting_mode">
36 <param name="sorting_mode_select" type="select" label="Sorting by" help="">
37 <option value="sortbylength">sequence length</option>
38 <option value="sortbyabundance">by abundance</option>
39 </param>
40 <when value="sortbylength">
41 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbylength)" />
42 </when>
43 <when value="sortbyabundance">
44 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbysize)" />
45 <param name="minsize" type="integer" value="" optional="True" label="Minimum abundance"
46 help="(--minsize)"/>
47 <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance"
48 help="(--maxsize)"/>
49 </when>
50 </conditional>
51 <expand macro="topn" />
52 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False"
53 label="Add abundance annotation to output" help="(--sizeout)"/>
54 </inputs>
55 <outputs>
56 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
57 </outputs>
58 <tests>
59 <test>
60 <param name="sorting_mode_select" value="sortbyabundance"/>
61 <param name="infile" value="db.fasta" ftype="fasta" />
62 <output name="outfile" file="sorting_result1.fasta" ftype="fasta" />
63 </test>
64 <test>
65 <param name="sorting_mode_select" value="sortbylength"/>
66 <param name="infile" value="db.fasta" ftype="fasta" />
67 <output name="outfile" file="sorting_result2.fasta" ftype="fasta" />
68 </test>
69 </tests>
70 <help>
71 <![CDATA[
72 **What it does**
73
74 Fasta entries are sorted by decreasing abundance (−−sortbysize) or sequence length (−−sort-
75 bylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and label
76 increasing alpha-numerical order (−−sortbylength), or just by label increasing alpha-numerical
77 order (−−sortbysize). Label sorting assumes that all sequences have unique labels. The same
78 applies to the automatic sorting performed during chimera checking (−−uchime_denovo), derepli-
79 cation (−−derep_fulllength), and clustering (−−cluster_fast and −−cluster_size).
80
81 Sorting options
82 --maxsize INT maximum abundance for sortbysize
83 --minsize INT minimum abundance for sortbysize
84 --output FILENAME output FASTA file
85 --relabel STRING relabel with this prefix string after sorting
86 --sizeout add abundance annotation to output
87 --sortbylength FILENAME sort sequences by length in given FASTA file
88 --sortbysize FILENAME abundance sort sequences in given FASTA file
89 --topn INT output just top n seqs after sorting
90
91
92 @EXTERNAL_DOCUMENTATION@
93
94 -------
95
96 @REFERENCES@
97
98
99 ]]>
100 </help>
101 <expand macro="citations" />
102 </tool>