Mercurial > repos > iuc > hmmer_hmmalign

annotate hmmalign.xml @ 3:a9c62fc8187b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:48:42 -0400
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17a98a843911 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_hmmalign" name="hmmalign" version="@TOOL_VERSION@">
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3 <description>align sequences to a profile HMM</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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10 hmmalign
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11
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12 $trim
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13 @FORMAT_SELECTOR@
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14 --outformat stockholm
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15
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16 '$hmmfile'
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17 '$seq'
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18 > '$output'
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19 ]]></command>
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20 <inputs>
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21 <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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22 <expand macro="input_hmm" />
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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23 <!-- TODO: mapali -->
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24 <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="trim terminal tails of nonaligned residues from alignment" />
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25 <expand macro="format_selector"/>
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26 </inputs>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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27 <outputs>
3
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28 <data name="output" format="stockholm" label="Alignment of $seq.name to $hmmfile.name" />
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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"/>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <param name="seq" value="globins45.fa"/>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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34 <output name="output" file="globins-45-align.sto" lines_diff="20"/>
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 @HELP_PRE@
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39
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40 Perform a multiple sequence alignment of all the sequences in <seqfile> by
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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41 aligning them individually to the profile HMM in <hmmfile>. The new alignment
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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42 is output to stdout in Stockholm format. The <hmmfile> should contain only a
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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43 single profile. If it contains more, only the first profile in the file will be
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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44 used.
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46 Either <hmmfile> or <seqfile> (but not both) may be ’-’ (dash), which means
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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47 reading this input from stdin rather than a file.
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48
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49 The sequences in <seqfile> are aligned in unihit local alignment mode.
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50 Therefore they should already be known to contain only a single domain (or a
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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51 fragment of one). The optimal alignment may assign some residues as
17a98a843911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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52 nonhomologous (N and C states), in which case these residues are still included
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53 in the resulting alignment, but shoved to the outer edges. To trim these
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54 unaligned nonhomologous residues from the result, see the --trim option.
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57 @HELP_PRE_OTH@
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59 @FORMAT_SELECTOR_HELP@
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61 @ATTRIBUTION@
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62 ]]></help>
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63 <expand macro="citation"/>
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64 </tool>