Mercurial > repos > iuc > hmmer_hmmfetch

annotate hmmfetch.xml @ 10:d3273f5e6b49 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:46:36 +0000
parents 939ad07a259c
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0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_hmmfetch" name="hmmfetch" version="@TOOL_VERSION@">
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d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <description>retrieve profile HMM(s) from a file</description>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <expand macro="bio_tools"/>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <macros>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <import>macros.xml</import>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 </macros>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <expand macro="requirements"/>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9 <expand macro="stdio"/>
d3273f5e6b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <command><![CDATA[
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11 hmmfetch -f '$hmmfile' '$keyfile' > '$output'
939ad07a259c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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12 ]]></command>
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0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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13 <inputs>
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14 <!-- TODO: implement auto-indexing -->
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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15 <expand macro="input_hmm" />
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16 <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
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17 </inputs>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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18 <outputs>
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19 <data name="output" format="hmm3" label="Selected HMM Models from $hmmfile.name">
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0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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20 </data>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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21 </outputs>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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22 <tests>
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23 <test>
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24 <param name="hmmfile" value="fn3.hmm"/>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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25 <param name="keyfile" value="fn3.keys"/>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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26 <output name="output" file="fn3.hmm" lines_diff="4"/>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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27 </test>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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28 </tests>
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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29 <help><![CDATA[
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30 @HELP_PRE@
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0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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32 Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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33 database, for example). The profile names should be listed in a text file,
0fa9130897ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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34 separated by newlines
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36 By default, fetched HMMs are printed to standard output in HMMER3 format.
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38 @ATTRIBUTION@
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39 ]]></help>
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40 <expand macro="citation"/>
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41 </tool>