Mercurial > repos > iuc > vsearch
comparison dereplication.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
| author | iuc |
|---|---|
| date | Thu, 17 Dec 2015 12:53:39 -0500 |
| parents | 8c4e2933a17a |
| children | 4258854759ba |
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| 1:8c4e2933a17a | 2:f29e21388219 |
|---|---|
| 1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1"> | 1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.2"> |
| 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" /> |
| 8 <expand macro="version_command" /> | 8 <expand macro="version_command" /> |
| 9 <command> | 9 <command> |
| 10 <![CDATA[ | 10 <![CDATA[ |
| 11 vsearch | 11 vsearch |
| 12 @GENERAL@ | 12 @GENERAL@ |
| 13 --derep_fulllength $infile | 13 --derep_fulllength "$infile" |
| 14 #if $maxuniquesize: | 14 #if str($maxuniquesize): |
| 15 --maxuniquesize $maxuniquesize | 15 --maxuniquesize "$maxuniquesize" |
| 16 #end if | 16 #end if |
| 17 #if $minuniquesize: | 17 #if str($minuniquesize): |
| 18 --minuniquesize $minuniquesize | 18 --minuniquesize "$minuniquesize" |
| 19 #end if | 19 #end if |
| 20 --output $outfile | 20 --output "$outfile" |
| 21 $sizein | 21 $sizein |
| 22 $sizeout | 22 $sizeout |
| 23 --strand $strand | 23 --strand "$strand" |
| 24 #if $topn: | 24 #if str($topn): |
| 25 --topn $topn | 25 --topn "$topn" |
| 26 #end if | 26 #end if |
| 27 #if $uc: | 27 #if $uc: |
| 28 --uc $uc_outfile | 28 --uc "$uc_outfile" |
| 29 #end if | 29 #end if |
| 30 ]]> | 30 ]]> |
| 31 </command> | 31 </command> |
| 32 <inputs> | 32 <inputs> |
| 33 <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)" /> |
| 97 --uc FILENAME filename for UCLUST-like output | 97 --uc FILENAME filename for UCLUST-like output |
| 98 | 98 |
| 99 | 99 |
| 100 @EXTERNAL_DOCUMENTATION@ | 100 @EXTERNAL_DOCUMENTATION@ |
| 101 | 101 |
| 102 ------- | |
| 103 | |
| 104 @REFERENCES@ | |
| 105 | |
| 106 | 102 |
| 107 ]]> | 103 ]]> |
| 108 </help> | 104 </help> |
| 109 <expand macro="citations" /> | 105 <expand macro="citations" /> |
| 110 </tool> | 106 </tool> |