Mercurial > repos > iuc > hmmer_hmmfetch
comparison hmmfetch.xml @ 0:0fa9130897ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
| author | iuc |
|---|---|
| date | Fri, 02 Oct 2015 13:40:40 -0400 |
| parents | |
| children | 939ad07a259c |
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| -1:000000000000 | 0:0fa9130897ff |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hmmer_hmmfetch" name="hmmfetch" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>retrieve profile HMM(s) from a file</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[ | |
| 10 hmmfetch -f $hmmfile $keyfile > $output; | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <!-- TODO: implement auto-indexing --> | |
| 14 <expand macro="input_hmm" /> | |
| 15 <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="hmm3" name="output" label="Selected HMM Models from $hmmfile.name"> | |
| 19 </data> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="hmmfile" value="fn3.hmm"/> | |
| 24 <param name="keyfile" value="fn3.keys"/> | |
| 25 <output name="output" file="fn3.hmm" lines_diff="4"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help><![CDATA[ | |
| 29 @HELP_PRE@ | |
| 30 | |
| 31 Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam | |
| 32 database, for example). The profile names should be listed in a text file, | |
| 33 separated by newlines | |
| 34 | |
| 35 By default, fetched HMMs are printed to standard output in HMMER3 format. | |
| 36 | |
| 37 @ATTRIBUTION@ | |
| 38 ]]></help> | |
| 39 <expand macro="citation"/> | |
| 40 </tool> |