annotate hmmconvert.xml @ 7:db8a5a3195e7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be"
author iuc
date Wed, 21 Jul 2021 14:13:43 +0000
parents 8d5ec58d2172
children d20066f6566e
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dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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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>
dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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4 <macros>
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5 <import>macros.xml</import>
dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 hmmconvert
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11 $format
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12 '$hmmfile'
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13 > '$output'
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14 ]]></command>
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dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 <inputs>
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16 <expand macro="input_hmm" />
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17 <param name="format" type="select" label="Output Format">
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18 <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
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19 <!--<option value="-b">output models in HMMER3 binary format</option>-->
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20 <option value="-2">backward compatible HMMER2 ASCII format</option>
dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="hmm3" label="$hmmfile.name">
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25 <change_format>
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26 <when input="format" value="-2" format="hmm2"/>
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27 </change_format>
dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="hmmfile" value="globins4.hmm"/>
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8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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33 <param name="format" value="-2" ftype="hmm2"/>
8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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34 <output name="output" file="globins4.hmm2" compare="sim_size">
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35 <assert_contents>
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36 <has_line_matching expression="HMMER2.*"/>
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37 <has_line_matching expression="ALPH Amino"/>
8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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38 <has_line_matching expression="NSEQ 4"/>
8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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39 <has_line_matching expression="//"/>
8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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40 </assert_contents>
8d5ec58d2172 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 @HELP_PRE@
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46
dca536c5cca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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47 The hmmconvert utility converts an input profile file to different HMMER formats.
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48
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49 By default, the input profile can be in any HMMER format, including
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50 old/obsolete formats from HMMER2, ASCII or binary; the output profile is a
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51 current HMMER3 ASCII format.
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52
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53 @ATTRIBUTION@
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54 ]]></help>
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55 <expand macro="citation"/>
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56 </tool>