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annotate hhblits.xml @ 3:35dbd62871b0 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:14:10 -0400
parents c3bf37da2daa
children 691d8f7c078c
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1 <tool id="hhblits" name="HH-blits" version="0.1.0" python_template_version="3.5">
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2 <description>itererative protein sequence searching</description>
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3 <requirements>
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4 <requirement type="package" version="3.2.0">hhsuite</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 link '$hhm_ffdata' hhdb_hhm.ffdata &&
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8 link '$hhm_ffindex' hhdb_hhm.ffindex &&
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9 link '$cs219_ffdata' hhdb_cs219.ffdata &&
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10 link '$cs219_ffindex' hhdb_cs219.ffindex &&
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11 hhblits -n '$n' -e '$e' -i '$input' -d hhdb -o '$output'
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12 ]]></command>
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13 <inputs>
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14 <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
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15 in a3m, a2m, or FASTA format, or HMM in hhm format (-i)"/>
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16 <param format="data" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'"/>
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17 <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'"/>
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18 <param format="data" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'"/>
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19 <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'"/>
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20 <param name="n" type="integer" label="Number of Iterations (-n)" value="2" min="1" max="8"/>
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21 <param name="e" type="float" label="E-value cutoff for inclusion in result alignment (-e)" value="0.001" min="0" max="1"/>
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22 </inputs>
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23 <outputs>
1
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24 <data format="data" name="output" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input" value="6VYB_A.fasta"/>
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29 <param name="hhm_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex"/>
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30 <param name="hhm_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata"/>
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31 <param name="cs219_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex"/>
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32 <param name="cs219_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata"/>
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33 <output name="output" file="6VYB_A.hhr" lines_diff="4"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 HMM-HMM-based lightning-fast iterative sequence search
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38 HHblits is a sensitive, general-purpose, iterative sequence search tool that represents
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39 both query and database sequences by HMMs. You can search HHblits databases starting
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40 with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits
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41 prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging
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42 the significant database HMMs/MSAs onto the query MSA.
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43
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44 Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
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45 ]]></help>
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46 <citations>
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47 <citation type="bibtex">
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48 @misc{githubhh-suite,
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49 author = {Soeding, Johannes},
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50 year = {2005},
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51 title = {Protein homology detection by HMM-HMM comparison},
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52 publisher = {Oxford University Press},
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53 journal = {Bioinformatics},
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54 url = {https://doi.org/10.1093/bioinformatics/bti125},
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55 }</citation>
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56 </citations>
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57 </tool>