Mercurial > repos > iuc > omark
annotate omark.xml @ 1:2eebe7f521f3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
author | iuc |
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date | Thu, 07 Mar 2024 18:22:16 +0000 |
parents | ce13b4c42256 |
children | 9607b69326e1 |
rev | line source |
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0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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changeset
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1 <?xml version="1.0"?> |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
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2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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3 <description>proteome quality assessment</description> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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4 <macros> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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5 <import>macros.xml</import> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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6 </macros> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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7 <requirements> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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8 <expand macro="requirements" /> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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changeset
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9 </requirements> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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10 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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11 <command detect_errors="exit_code"><![CDATA[ |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
parents:
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12 omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer' |
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
parents:
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13 |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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14 && |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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15 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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16 omark |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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17 -f 'output_omamer' |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
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18 -d '$database.fields.path' |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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19 $omark_mode |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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20 -i '$input_iso' |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
parents:
0
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21 -t '$t' |
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
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22 -r '$r' |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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23 -o omark_galaxy |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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24 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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25 ]]></command> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
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26 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
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27 <inputs> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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changeset
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28 <param name="input" type="data" format="fasta" label="Protein sequences"/> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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29 <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/> |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
parents:
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30 <param argument="-c" name="omark_mode" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/> |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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changeset
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31 <param name="database" label="OMAmer database" type="select"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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32 <options from_data_table="omamer"/> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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33 </param> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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34 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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35 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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36 <sanitizer invalid_char=""> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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37 <valid initial="string.letters,string.digits"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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38 <add value="_" /> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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39 </valid> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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40 </sanitizer> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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41 <validator type="regex">[0-9a-zA-Z_]+</validator> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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42 </param> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
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43 <param argument="-r" type="text" optional="true" label="Taxonomic rank"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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44 <sanitizer invalid_char=""> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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45 <valid initial="string.letters,string.digits"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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46 <add value="_" /> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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47 </valid> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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48 </sanitizer> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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49 <validator type="regex">[0-9a-zA-Z_]+</validator> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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50 </param> |
1
2eebe7f521f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
iuc
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51 |
0
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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52 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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53 <option value="detail_sum" selected="true">Detailed summary</option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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54 <option value="hog">HOG identifiers</option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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55 <option value="pdf">PDF Graphic representation </option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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56 <option value="png">PNG Graphic representation </option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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57 <option value="sum">Comparative proteome analysis</option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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58 <option value="tax">Taxomony</option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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59 <option value="ump">Protein identifiers</option> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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60 </param> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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61 </inputs> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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62 |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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63 <outputs> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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64 <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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65 <filter>outputs and 'detail_sum' in outputs</filter> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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66 </data> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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67 <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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68 <filter>outputs and 'hog' in outputs</filter> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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69 </data> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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70 <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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71 <filter>outputs and 'pdf' in outputs</filter> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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72 </data> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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73 <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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74 <filter>outputs and 'png' in outputs</filter> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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75 </data> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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76 <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
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77 <filter>outputs and 'sum' in outputs</filter> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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78 </data> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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79 <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax"> |
ce13b4c42256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
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80 <filter>outputs and 'tax' in outputs</filter> |
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81 </data> |
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82 <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump"> |
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83 <filter>outputs and 'ump' in outputs</filter> |
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84 </data> |
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85 </outputs> |
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86 |
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87 <tests> |
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88 <test expect_failure="true"> |
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89 <param name="input" value="input.fasta"/> |
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90 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/> |
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91 <param name="database" value="test"/> |
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92 |
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93 <!-- Couldn't create a minimal working hdf5 dataset --> |
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94 <assert_stderr> |
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95 <has_text text="file signature not found"/> |
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96 <has_text text="End of HDF5 error back trace" /> |
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97 </assert_stderr> |
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98 </test> |
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99 </tests> |
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100 |
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101 |
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102 <help><![CDATA[ |
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103 OMark_: is a software for proteome quality assessment. |
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104 It provides measures of proteome completeness, characterizes the consistency |
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105 of all protein coding genes with regard to their homologs, and identifies the |
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106 presence of contamination from other species. |
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107 |
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108 OMArk relies on the OMA orthology database. |
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109 For more information, please refer to the OMamer_ documentaion. |
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110 |
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111 .. _OMark: https://github.com/DessimozLab/OMArk |
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112 .. _OMamer: https://github.com/DessimozLab/omamer |
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113 ]]></help> |
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114 <expand macro="citation"/> |
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115 </tool> |