Mercurial > repos > iuc > kofamscan
annotate kofamscan.xml @ 0:24adf43898ec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
author | iuc |
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date | Fri, 15 Jan 2021 10:48:52 +0000 |
parents | |
children | 23494763e39e |
rev | line source |
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0
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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changeset
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1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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2 <description>gene function annotation based on KEGG orthology and HMM</description> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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3 <macros> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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4 <token name="@TOOL_VERSION@">1.3.0</token> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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5 <token name="@VERSION_SUFFIX@">0</token> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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6 <xml name="reportannotation" token_selected=""> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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8 </xml> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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9 </macros> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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10 <requirements> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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11 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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12 <requirement type="package" version="3.0">zip</requirement> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
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13 </requirements> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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14 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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15 <command detect_errors="exit_code"><![CDATA[ |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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16 ## preprocessing |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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17 mkdir 'profile' && |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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18 #if $p_cond.p_sel == 'compressed' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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19 tar -xf '${p_cond.p}' -C 'profile' && |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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20 #elif $p_cond.p_sel == 'hmm' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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21 ## input files require prefix 'K' and file extension '.hmm' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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22 #for $i, $current in enumerate($p_cond.p) |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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23 ln -s '$current' 'profile/K${i}.hmm' && |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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24 #end for |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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25 #end if |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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26 |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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27 ## run |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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28 exec_annotation |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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29 -p 'profile' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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30 -o 'result.txt' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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31 -k '$k' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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32 --cpu \${GALAXY_SLOTS:-4} |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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33 -E $E |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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34 -T $ap.T |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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35 -f '$ap.f_cond.f_sel' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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36 $ap.f_cond.reportannotation |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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37 #if 'alignments' in $ap.out |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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38 --create-alignment |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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39 #end if |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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40 '$query' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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41 |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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42 ## postprocessing |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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43 #if 'alignments' in $ap.out |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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44 && test -d 'tmp/alignment' && zip -q -r 'tmp/alignments.zip' tmp/alignment/* || echo 'No alignment files.' |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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45 #end if |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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46 ]]></command> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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47 <inputs> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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48 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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49 <conditional name="p_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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50 <param name="p_sel" type="select" label="Select profile database format"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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51 <option value="compressed" selected="true">Compressed set of HMM and HAL file(s)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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52 <option value="hmm">HMM file(s)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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53 </param> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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54 <when value="compressed"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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55 <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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56 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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57 <when value="hmm"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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58 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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59 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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60 </conditional> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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61 <param argument="-k" type="data" format="tabular" label="Select KO list file"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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62 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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63 <section name="ap" title="Advanced parameters" expanded="true"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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64 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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65 <conditional name="f_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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66 <param name="f_sel" type="select" label="Select output format"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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67 <option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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68 <option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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69 <option value="mapper">KEGG Mapper compatible format (mapper)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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70 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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71 </param> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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72 <when value="detail"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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73 <expand macro="reportannotation" selected="false"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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74 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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75 <when value="detail-tsv"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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76 <expand macro="reportannotation" selected="false"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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77 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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78 <when value="mapper"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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79 <expand macro="reportannotation" selected="true"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
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80 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
81 <when value="mapper-one-line"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
82 <expand macro="reportannotation" selected="true"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
83 </when> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
84 </conditional> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
85 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run."> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
86 <option value="result" selected="true">KofamScan Result</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
87 <option value="alignments">HMMER alignments</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
88 <option value="output">HMMER run output</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
89 <option value="tabular">HMMER tabular summary</option> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
90 </param> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
91 </section> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
92 </inputs> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
93 <outputs> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
94 <data name="out_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
95 <filter>'alignments' in ap['out']</filter> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
96 </data> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
97 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
98 <filter>'output' in ap['out']</filter> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
99 </data> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
100 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
101 <filter>'result' in ap['out']</filter> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
102 </data> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
103 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${tool.name} on ${on_string}: HMMER tabular"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
104 <filter>'tabular' in ap['out']</filter> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
105 </data> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
106 </outputs> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
107 <tests> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
108 <!-- #1 default --> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
109 <test expect_num_outputs="1"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
110 <param name="query" value="query.fasta"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
111 <conditional name="p_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
112 <param name="p_sel" value="compressed"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
113 <param name="p" value="profiles.tar.gz"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
114 </conditional> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
115 <param name="k" value="ko"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
116 <output name="out_result"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
117 <assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
118 <has_n_lines n="5"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
119 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
120 </assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
121 </output> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
122 </test> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
123 <!-- #2 --> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
124 <test expect_num_outputs="4"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
125 <param name="query" value="query.fasta"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
126 <conditional name="p_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
127 <param name="p_sel" value="hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
128 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
129 </conditional> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
130 <param name="k" value="ko"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
131 <param name="E" value="0.02"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
132 <section name="ap"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
133 <param name="T" value="2"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
134 <conditional name="f_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
135 <param name="f_sel" value="detail-tsv"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
136 <param name="reportannotation" value="true"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
137 </conditional> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
138 <param name="out" value="alignments,output,result,tabular"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
139 </section> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
140 <output name="out_alignments"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
141 <assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
142 <has_size value="4099"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
143 </assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
144 </output> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
145 <output name="out_output"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
146 <assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
147 <has_n_lines n="224"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
148 <has_line line="Internal pipeline statistics summary:"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
149 </assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
150 </output> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
151 <output name="out_result"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
152 <assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
153 <has_n_lines n="9"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
154 <has_text_matching expression=".+sp\|P19858\|LDHA_BOVIN"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
155 </assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
156 </output> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
157 <output name="out_tabular"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
158 <assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
159 <has_n_lines n="48"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
160 <has_line line="K1"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
161 </assert_contents> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
162 </output> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
163 </test> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff
changeset
|
164 <!-- #3 --> |
24adf43898ec
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165 <test expect_num_outputs="1"> |
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166 <param name="query" value="query.fasta"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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167 <conditional name="p_cond"> |
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168 <param name="p_sel" value="hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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169 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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170 </conditional> |
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171 <param name="k" value="ko"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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172 <section name="ap"> |
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173 <conditional name="f_cond"> |
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174 <param name="f_sel" value="mapper"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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175 </conditional> |
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176 </section> |
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177 <output name="out_result"> |
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178 <assert_contents> |
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179 <has_n_lines n="7"/> |
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180 <has_line line="sp|P19858|LDHA_BOVIN"/> |
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181 </assert_contents> |
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182 </output> |
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183 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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184 <!-- #4 --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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185 <test expect_num_outputs="1"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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186 <param name="query" value="query.fasta"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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187 <conditional name="p_cond"> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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188 <param name="p_sel" value="hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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189 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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190 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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191 <param name="k" value="ko"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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192 <section name="ap"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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193 <conditional name="f_cond"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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194 <param name="f_sel" value="mapper-one-line"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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195 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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196 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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197 <output name="out_result"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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198 <assert_contents> |
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199 <has_n_lines n="7"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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200 <has_line line="sp|P19858|LDHA_BOVIN"/> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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201 </assert_contents> |
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202 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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203 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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204 </tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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205 <help><![CDATA[ |
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206 .. class:: infomark |
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207 |
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208 **What it does** |
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209 |
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210 KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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211 |
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212 KofamScan assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers. |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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213 |
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214 **Input** |
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215 |
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216 - a query file in FASTA format with one or more amino acid sequences. Each sequence must have a unique name. A name of a sequence is a string between the header symbol (">") and the first blank character (whitespace, tab, line break, etc.). Do not put a whitespace right after ">". |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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217 |
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218 :: |
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219 |
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220 >sp|P00325|ADH1B_HUMAN Alcohol dehydrogenase 1B OS=Homo sapiens GN=ADH1B PE=1 SV=2 |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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221 MSTAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVT |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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222 |
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223 - a KO list file of KOfam |
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224 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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225 :: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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226 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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227 knum threshold score_type profile_type F-measure nseq nseq_used alen mlen eff_nseq re/pos definition |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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228 K00001 361.33 domain trim 0.326825 1601 1149 1538 393 13.33 0.590 alcohol dehydrogenase [EC:1.1.1.1] |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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229 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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230 - KOfam profile files in HMM3 format or a compressed dataset containing HMM3 profiles and HAL filtering files available `here <ftp://ftp.genome.jp/pub/db/kofam/>`_. |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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231 |
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232 **Output** |
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233 |
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234 - KofamScan output |
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235 - HMMER results as alignments, run output and tabular summary |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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236 |
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237 .. class:: infomark |
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238 |
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239 **References** |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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240 |
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241 More information are available on `GitHub <https://github.com/takaram/kofam_scan>`_ and the `KofamKOALA webserver <https://www.genome.jp/tools/kofamkoala/>`_. |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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242 ]]></help> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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243 <citations> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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244 <citation type="doi">10.1093/bioinformatics/btz859</citation> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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245 </citations> |
24adf43898ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
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246 </tool> |