Mercurial > repos > iuc > vsearch

annotate sorting.xml @ 6:9495df9dd6ef draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:36:19 +0000
parents 4258854759ba
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
1 <tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0">
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
2 <description></description>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
4 <import>vsearch_macros.xml</import>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
8 <expand macro="version_command" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
9 <command>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
10 <![CDATA[
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
11 vsearch
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
12 @GENERAL@
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
13 #if $sorting_mode.sorting_mode_select == 'sortbylength':
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
14 --sortbylength "$sorting_mode.infile"
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
15 #else:
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
16 --sortbysize "$sorting_mode.infile"
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
17 #if str( $sorting_mode.minsize ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
18 --minsize "$sorting_mode.minsize"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
19 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
20 #if str( $sorting_mode.maxsize ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
21 --maxsize "$sorting_mode.maxsize"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
22 #end if
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
23 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
24 --output "$outfile"
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
25 #if $relabel:
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
26 --relabel "$relabel"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
27 #end if
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
28 $sizeout
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
29 #if str( $topn ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
30 --topn "$topn"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
31 #end if
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
32
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
33 ]]>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
34 </command>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
35 <inputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
36 <conditional name="sorting_mode">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
37 <param name="sorting_mode_select" type="select" label="Sorting by" help="">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
38 <option value="sortbylength">sequence length</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
39 <option value="sortbyabundance">by abundance</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
40 </param>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
41 <when value="sortbylength">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
42 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbylength)" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
43 </when>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
44 <when value="sortbyabundance">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
45 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbysize)" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
46 <param name="minsize" type="integer" value="" optional="True" label="Minimum abundance"
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
47 help="(--minsize)"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
48 <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance"
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
49 help="(--maxsize)"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
50 </when>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
51 </conditional>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
52 <expand macro="topn" />
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
53 <param name="relabel" type="text" value=""
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
54 label="Relabel with this prefix string after sorting" help="(--relabel)"/>
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
55 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False"
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
56 label="Add abundance annotation to output" help="(--sizeout)"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
57 </inputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
58 <outputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
59 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
60 </outputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
61 <tests>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
62 <test>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
63 <param name="sorting_mode_select" value="sortbyabundance"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
64 <param name="infile" value="db.fasta" ftype="fasta" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
65 <output name="outfile" file="sorting_result1.fasta" ftype="fasta" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
66 </test>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
67 <test>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
68 <param name="sorting_mode_select" value="sortbylength"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
69 <param name="infile" value="db.fasta" ftype="fasta" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
70 <output name="outfile" file="sorting_result2.fasta" ftype="fasta" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
71 </test>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
72 <test>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
73 <param name="sorting_mode_select" value="sortbylength"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
74 <param name="infile" value="db.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
75 <param name="relabel" value="TEST" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
76 <output name="outfile" file="sorting_result3.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
77 </test>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
78 <test>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
79 <param name="sorting_mode_select" value="sortbylength"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
80 <param name="infile" value="db.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
81 <param name="sizeout" value="--sizeout" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
82 <output name="outfile" file="sorting_result4.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
83 </test>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
84 <test>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
85 <param name="sorting_mode_select" value="sortbylength"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
86 <param name="infile" value="db.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
87 <param name="relabel" value="With spaces" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
88 <output name="outfile" file="sorting_result5.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
89 </test>
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
90 </tests>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
91 <help>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
92 <![CDATA[
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
93 **What it does**
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
94
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
95 Fasta entries are sorted by decreasing abundance (−−sortbysize) or sequence length (−−sort-
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
96 bylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and label
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
97 increasing alpha-numerical order (−−sortbylength), or just by label increasing alpha-numerical
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
98 order (−−sortbysize). Label sorting assumes that all sequences have unique labels. The same
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
99 applies to the automatic sorting performed during chimera checking (−−uchime_denovo), derepli-
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
100 cation (−−derep_fulllength), and clustering (−−cluster_fast and −−cluster_size).
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
101
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
102 Sorting options
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
103 --maxsize INT maximum abundance for sortbysize
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
104 --minsize INT minimum abundance for sortbysize
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
105 --output FILENAME output FASTA file
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
106 --relabel STRING relabel with this prefix string after sorting
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
107 --sizeout add abundance annotation to output
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
108 --sortbylength FILENAME sort sequences by length in given FASTA file
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
109 --sortbysize FILENAME abundance sort sequences in given FASTA file
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
110 --topn INT output just top n seqs after sorting
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
111
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
112
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
113 @EXTERNAL_DOCUMENTATION@
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
114
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
115
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
116 ]]>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
117 </help>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
118 <expand macro="citations" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
119 </tool>