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annotate kofamscan.xml @ 2:95c71179a054 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 01b23e76826616bee43b50fd73bb259347537056
author iuc
date Mon, 11 Mar 2024 15:28:15 +0000
parents 23494763e39e
children c3c46f14c7a4
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1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>gene function annotation based on KEGG orthology and HMM</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.0</token>
1
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 <xml name="reportannotation" token_selected="">
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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?"/>
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8 </xml>
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9 </macros>
2
95c71179a054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 01b23e76826616bee43b50fd73bb259347537056
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10 <xrefs>
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11 <xref type="bio.tools">kofamscan</xref>
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12 </xrefs>
0
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13 <requirements>
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14 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement>
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15 <requirement type="package" version="3.0">zip</requirement>
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16 </requirements>
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17 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
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18 <command detect_errors="exit_code"><![CDATA[
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19 ## preprocessing
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20 mkdir ./profile &&
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21 mkdir ./temp_extract &&
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22 #if $p_cond.p_sel == 'compressed'
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23 tar -xf '${p_cond.p}' -C temp_extract &&
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24 find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; &&
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25 find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; &&
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26 #elif $p_cond.p_sel == 'hmm'
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27 ## input files require prefix 'K' and file extension '.hmm'
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28 #for $i, $current in enumerate($p_cond.p)
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29 ln -s '$current' 'profile/K${i}.hmm' &&
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30 #end for
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31 #end if
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32
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33 ## run
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34 exec_annotation
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35 -p 'profile'
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36 -o 'result.txt'
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37 -k '$k'
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38 --cpu \${GALAXY_SLOTS:-4}
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39 -E $E
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40 -T $ap.T
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41 -f '$ap.f_cond.f_sel'
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42 $ap.f_cond.reportannotation
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43 #if 'alignments' in $ap.out
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44 --create-alignment
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45 #end if
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46 '$query'
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47
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48 ## postprocessing
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49 #if 'alignments' in $ap.out
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50 && test -d 'tmp/alignment' && zip -q -r 'tmp/alignments.zip' tmp/alignment/* || echo 'No alignment files.'
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51 #end if
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52 ]]></command>
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53 <inputs>
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54 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/>
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55 <conditional name="p_cond">
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56 <param name="p_sel" type="select" label="Select profile database format">
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57 <option value="compressed" selected="true">Compressed set of HMM and HAL file(s)</option>
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58 <option value="hmm">HMM file(s)</option>
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59 </param>
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60 <when value="compressed">
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61 <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/)."/>
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62 </when>
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63 <when value="hmm">
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64 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/>
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65 </when>
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66 </conditional>
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67 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
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68 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/>
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69 <section name="ap" title="Advanced parameters" expanded="true">
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70 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
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71 <conditional name="f_cond">
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72 <param name="f_sel" type="select" label="Select output format">
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73 <option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option>
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74 <option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option>
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75 <option value="mapper">KEGG Mapper compatible format (mapper)</option>
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76 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
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77 </param>
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78 <when value="detail">
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79 <expand macro="reportannotation" selected="false"/>
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80 </when>
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81 <when value="detail-tsv">
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82 <expand macro="reportannotation" selected="false"/>
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83 </when>
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84 <when value="mapper">
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85 <expand macro="reportannotation" selected="true"/>
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86 </when>
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iuc
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diff changeset
87 <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
88 <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
89 </when>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
90 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
91 <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
92 <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
93 <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
94 <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
95 <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
96 </param>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
97 </section>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
98 </inputs>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
99 <outputs>
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_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
101 <filter>'alignments' in ap['out']</filter>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
102 </data>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
103 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
104 <filter>'output' in ap['out']</filter>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
105 </data>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
106 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
107 <filter>'result' in ap['out']</filter>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
108 </data>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
109 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${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
110 <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
111 </data>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
112 </outputs>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
113 <tests>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
114 <!-- #1 default -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
115 <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
116 <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
117 <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
118 <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
119 <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
120 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
121 <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
122 <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
123 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
124 <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
125 <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
126 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
127 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
128 </test>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
129 <!-- #2 -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
130 <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
131 <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
132 <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
133 <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
134 <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
135 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
136 <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
137 <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
138 <section name="ap">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
139 <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
140 <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
141 <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
142 <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
143 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
144 <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
145 </section>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
146 <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
147 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
148 <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
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_output">
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="224"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
154 <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
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_result">
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="9"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
160 <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
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 <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
164 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
165 <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
166 <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
167 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
168 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
169 </test>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
170 <!-- #3 -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
171 <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
172 <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
173 <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
174 <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
175 <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
176 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
177 <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
178 <section name="ap">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
179 <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
180 <param name="f_sel" value="mapper"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
181 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
182 </section>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
183 <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
184 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
185 <has_n_lines n="7"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
186 <has_line line="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
187 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
188 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
189 </test>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
190 <!-- #4 -->
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
191 <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
192 <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
193 <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
194 <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
195 <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
196 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
197 <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
198 <section name="ap">
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
199 <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
200 <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"
iuc
parents:
diff changeset
201 </conditional>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
202 </section>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
203 <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
204 <assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
205 <has_n_lines n="7"/>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
206 <has_line line="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
207 </assert_contents>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
208 </output>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
209 </test>
1
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
210 <!-- #5 -->
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
211 <test expect_num_outputs="1">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
212 <param name="query" value="query.fasta"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
213 <conditional name="p_cond">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
214 <param name="p_sel" value="compressed"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
215 <param name="p" value="profilesTyp2.tar.gz"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
216 </conditional>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
217 <param name="k" value="ko"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
218 <output name="out_result">
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
219 <assert_contents>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
220 <has_n_lines n="5"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
221 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
222 </assert_contents>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
223 </output>
23494763e39e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
iuc
parents: 0
diff changeset
224 </test>
0
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
225 </tests>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
226 <help><![CDATA[
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
227 .. class:: infomark
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
228
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
229 **What it does**
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
230
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
231 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"
iuc
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diff changeset
232
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
233 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"
iuc
parents:
diff changeset
234
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
235 **Input**
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
236
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
237 - 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"
iuc
parents:
diff changeset
238
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
239 ::
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
240
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
241 >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"
iuc
parents:
diff changeset
242 MSTAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVT
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
243
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
244 - a KO list file of KOfam
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
245
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
246 ::
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
247
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
248 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"
iuc
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diff changeset
249 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"
iuc
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diff changeset
250
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
251 - 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"
iuc
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diff changeset
252
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
253 **Output**
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
254
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
255 - KofamScan output
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
256 - 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"
iuc
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diff changeset
257
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
258 .. class:: infomark
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
259
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
260 **References**
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
261
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
262 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"
iuc
parents:
diff changeset
263 ]]></help>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
264 <citations>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
parents:
diff changeset
265 <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"
iuc
parents:
diff changeset
266 </citations>
24adf43898ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
iuc
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diff changeset
267 </tool>