Mercurial > repos > iuc > hmmer_hmmalign

comparison hmmalign.xml @ 3:a9c62fc8187b draft

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/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:48:42 -0400
parents 17a98a843911
children 9319e9ed248b
comparison
equal deleted inserted replaced
2:2e7a30181368 3:a9c62fc8187b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmalign" name="hmmalign" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_hmmalign" name="hmmalign" version="@TOOL_VERSION@">
3 <description>align sequences to a profile HMM</description> 3 <description>align sequences to a profile HMM</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
11 11
12 $trim 12 $trim
13 @FORMAT_SELECTOR@ 13 @FORMAT_SELECTOR@
14 --outformat stockholm 14 --outformat stockholm
15 15
16 $hmmfile 16 '$hmmfile'
17 $seq 17 '$seq'
18 > $output 18 > '$output'
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/> 21 <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/>
22 <expand macro="input_hmm" /> 22 <expand macro="input_hmm" />
23 <!-- TODO: mapali --> 23 <!-- TODO: mapali -->
24 <param name="trim" type="boolean" truevalue="--trim" label="trim terminal tails of nonaligned residues from alignment" help="(--trim)" falsevalue=""/> 24 <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="trim terminal tails of nonaligned residues from alignment" />
25 <expand macro="format_selector"/> 25 <expand macro="format_selector"/>
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data format="stockholm" name="output" label="Alignment of $seq.name to $hmmfile.name"> 28 <data name="output" format="stockholm" label="Alignment of $seq.name to $hmmfile.name" />
29 </data>
30 </outputs> 29 </outputs>
31 <tests> 30 <tests>
32 <test> 31 <test>
33 <param name="hmmfile" value="globins4.hmm"/> 32 <param name="hmmfile" value="globins4.hmm"/>
34 <param name="seq" value="globins45.fa"/> 33 <param name="seq" value="globins45.fa"/>
58 @HELP_PRE_OTH@ 57 @HELP_PRE_OTH@
59 58
60 @FORMAT_SELECTOR_HELP@ 59 @FORMAT_SELECTOR_HELP@
61 60
62 @ATTRIBUTION@ 61 @ATTRIBUTION@
63 ]]></help> 62 ]]></help>
64 <expand macro="citation"/> 63 <expand macro="citation"/>
65 </tool> 64 </tool>