Mercurial > repos > iuc > hmmer3

annotate hmmfetch.xml @ 2:ef9501a30bfe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:23:53 -0400
parents 79523243a079
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afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
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1 <?xml version="1.0"?>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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2 <tool id="hmmer_hmmfetch" name="hmmfetch" version="@WRAPPER_VERSION@.0">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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3 <description>retrieve profile HMM(s) from a file</description>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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4 <macros>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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5 <import>macros.xml</import>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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6 </macros>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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7 <expand macro="requirements"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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8 <expand macro="stdio"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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9 <command><![CDATA[
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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10 hmmfetch -f $hmmfile $keyfile > $output;
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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11 ]]></command>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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12 <inputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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13 <!-- TODO: implement auto-indexing -->
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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14 <expand macro="input_hmm" />
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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15 <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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16 </inputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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17 <outputs>
1
79523243a079 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 45a64d82dfada34d826be98a1f7a0657f9148d59
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18 <data format="hmm3" name="output" label="Selected HMM Models from $hmmfile.name">
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afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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19 </data>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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20 </outputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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21 <tests>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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22 <test>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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23 <param name="hmmfile" value="fn3.hmm"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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24 <param name="keyfile" value="fn3.keys"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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25 <output name="output" file="fn3.hmm" lines_diff="4"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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26 </test>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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27 </tests>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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28 <help><![CDATA[
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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29 @HELP_PRE@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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30
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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31 Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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32 database, for example). The profile names should be listed in a text file,
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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33 separated by newlines
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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34
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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35 By default, fetched HMMs are printed to standard output in HMMER3 format.
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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36
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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37 @ATTRIBUTION@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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38 ]]></help>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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39 <expand macro="citation"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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40 </tool>