Mercurial > repos > iuc > hmmer_hmmconvert

annotate hmmconvert.xml @ 10:48271926403d 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 08:42:03 +0000
parents 0a01f9fa3453
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_hmmconvert" name="hmmconvert" version="@TOOL_VERSION@">
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3 <description>convert profile file to a HMMER format</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 hmmconvert
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12 $format
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13 '$hmmfile'
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14 > '$output'
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15 ]]></command>
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16 <inputs>
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17 <expand macro="input_hmm" />
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18 <param name="format" type="select" label="Output Format">
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19 <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
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20 <!--<option value="-b">output models in HMMER3 binary format</option>-->
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21 <option value="-2">backward compatible HMMER2 ASCII format</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="hmm3" label="$hmmfile.name">
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26 <change_format>
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27 <when input="format" value="-2" format="hmm2"/>
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28 </change_format>
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29 </data>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="hmmfile" value="globins4.hmm"/>
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34 <param name="format" value="-2" ftype="hmm2"/>
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35 <output name="output" file="globins4.hmm2" compare="sim_size">
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36 <assert_contents>
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37 <has_line_matching expression="HMMER2.*"/>
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38 <has_line_matching expression="ALPH Amino"/>
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39 <has_line_matching expression="NSEQ 4"/>
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40 <has_line_matching expression="//"/>
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41 </assert_contents>
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42 </output>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 @HELP_PRE@
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47
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48 The hmmconvert utility converts an input profile file to different HMMER formats.
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49
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50 By default, the input profile can be in any HMMER format, including
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51 old/obsolete formats from HMMER2, ASCII or binary; the output profile is a
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52 current HMMER3 ASCII format.
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53
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54 @ATTRIBUTION@
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55 ]]></help>
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56 <expand macro="citation"/>
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57 </tool>