Mercurial > repos > iuc > vsearch
annotate chimera.xml @ 6:9495df9dd6ef draft default tip
"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 |
| rev | line source |
|---|---|
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4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
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changeset
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1 <tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0"> |
| 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@ | |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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13 --abskew "${abskew}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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14 --chimeras "${outfile}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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15 --dn "${dn}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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16 --mindiffs "${mindiffs}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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17 --mindiv "${mindiv}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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18 --minh "${minh}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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19 --xn "${xn}" |
| 0 | 20 $self_param |
| 21 $selfid_param | |
| 22 #if $detection_mode.detection_mode_select == 'denovo': | |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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23 --uchime_denovo "${detection_mode.infile_denovo}" |
| 0 | 24 #else: |
| 25 --uchime_ref $detection_mode.infile_reference | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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26 --db "${detection_mode.db}" |
| 0 | 27 #end if |
| 28 | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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29 #if 'nonchimeras' in str($outputs).split( "," ): |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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30 --nonchimeras "${nonchimeras}" |
| 0 | 31 #end if |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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32 #if 'uchimealns' in str($outputs).split( "," ): |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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33 --uchimealns "${uchimealns}" |
| 0 | 34 #end if |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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35 #if 'uchimeout' in str($outputs).split( "," ): |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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36 --uchimeout "${uchimeout}" |
| 0 | 37 #end if |
| 38 | |
| 39 ]]> | |
| 40 </command> | |
| 41 <inputs> | |
| 42 <conditional name="detection_mode"> | |
| 43 <param name="detection_mode_select" type="select" label="Detect chimeras" help=""> | |
| 44 <option value="denovo">de novo</option> | |
| 45 <option value="reference">using a reference database</option> | |
| 46 </param> | |
| 47 <when value="denovo"> | |
| 48 <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" /> | |
| 49 </when> | |
| 50 <when value="reference"> | |
| 51 <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" /> | |
| 52 <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" /> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 | |
| 56 <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera" | |
| 57 help="(--abskew)"/> | |
| 58 <param name="dn" type="float" value="1.4" label="'no' vote pseudo count" | |
| 59 help="(--dn)"/> | |
| 60 <param name="xn" type="float" value="8.0" label="'no' vote weight" | |
| 61 help="(--xn)"/> | |
| 62 <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment" | |
| 63 help="(--mindiffs)"/> | |
| 64 <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent" | |
| 65 help="(--mindiv)"/> | |
| 66 <param name="minh" type="float" value="0.28" label="Minimum score" | |
| 67 help="(--minh)"/> | |
| 68 | |
| 69 <expand macro="self_and_selfid" /> | |
| 70 | |
| 71 <param name="outputs" type="select" multiple="True" optional="True" | |
| 72 label="Select output formats" help="(--qmask)"> | |
| 73 <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option> | |
| 74 <option value="uchimealns">Chimera alignments (--uchimealns)</option> | |
| 75 <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option> | |
| 76 </param> | |
| 77 | |
| 78 </inputs> | |
| 79 <outputs> | |
| 80 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> | |
| 81 <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera"> | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
82 <filter>outputs and 'nonchimeras' in outputs</filter> |
| 0 | 83 </data> |
| 84 <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments"> | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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85 <filter>outputs and 'uchimealns' in outputs</filter> |
| 0 | 86 </data> |
| 87 <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information"> | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
88 <filter>outputs and 'uchimeout' in outputs</filter> |
| 0 | 89 </data> |
| 90 </outputs> | |
| 91 <tests> | |
| 92 <test> | |
| 93 <param name="detection_mode_select" value="denovo"/> | |
| 94 <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" /> | |
| 95 <param name="outputs" value="uchimeout"/> | |
| 96 <output name="outfile" file="chimera_result1.fasta" ftype="fasta" /> | |
| 97 <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" /> | |
| 98 </test> | |
| 99 </tests> | |
| 100 <help> | |
| 101 <![CDATA[ | |
| 102 **What it does** | |
| 103 | |
| 104 Sequence chimera detection based on a different scoring functions. | |
| 105 | |
| 106 Chimera detection options | |
| 107 --abskew REAL min abundance ratio of parent vs chimera (2.0) | |
| 108 --alignwidth INT width of alignment in uchimealn output (80) | |
| 109 --chimeras FILENAME output chimeric sequences to file | |
| 110 --db FILENAME reference database for --uchime_ref | |
| 111 --dn REAL 'no' vote pseudo-count (1.4) | |
| 112 --mindiffs INT minimum number of differences in segment (3) | |
| 113 --mindiv REAL minimum divergence from closest parent (0.8) | |
| 114 --minh REAL minimum score (0.28) | |
| 115 --nonchimeras FILENAME output non-chimeric sequences to file | |
| 116 --self exclude identical labels for --uchime_ref | |
| 117 --selfid exclude identical sequences for --uchime_ref | |
| 118 --uchime_denovo FILENAME detect chimeras de novo | |
| 119 --uchime_ref FILENAME detect chimeras using a reference database | |
| 120 --uchimealns FILENAME output chimera alignments to file | |
| 121 --uchimeout FILENAME output to chimera info to tab-separated file | |
| 122 --uchimeout5 make output compatible with uchime version 5 | |
| 123 --xn REAL 'no' vote weight (8.0) | |
| 124 | |
| 125 @EXTERNAL_DOCUMENTATION@ | |
| 126 | |
| 127 | |
| 128 ]]> | |
| 129 </help> | |
| 130 <expand macro="citations" /> | |
| 131 </tool> |