Mercurial > repos > iuc > checkm_taxonomy_wf
annotate taxonomy_wf.xml @ 2:19e4e2d98ebb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
author | iuc |
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date | Mon, 02 Sep 2024 13:51:50 +0000 |
parents | 2e995a9aa00e |
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rev | line source |
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0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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1 <tool id="checkm_taxonomy_wf" name="CheckM taxonomy_wf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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2 <description> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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|
3 Analyze all genome bins with the same marker set |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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|
4 </description> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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5 <macros> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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6 <import>macros.xml</import> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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7 </macros> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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changeset
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8 <expand macro="biotools"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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9 <expand macro="requirements"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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10 <expand macro="version"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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11 <command detect_errors="exit_code"><![CDATA[ |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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12 @BIN_INPUTS@ |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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13 |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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14 checkm taxonomy_wf |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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15 '$rank_taxon.rank' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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16 '$rank_taxon.taxon.fields.value' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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17 'bins' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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18 'output' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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19 $analyze.ali |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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20 $analyze.nt |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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21 $analyze.genes |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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22 $qa.individual_markers |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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23 $qa.skip_adj_correction |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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24 $qa.skip_pseudogene_correction |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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changeset
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25 --aai_strain $qa.aai_strain |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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26 $qa.ignore_thresholds |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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27 --e_value $qa.e_value |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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28 --length $qa.length |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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29 --file '$results' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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30 --tab_table |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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31 --extension 'fasta' |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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32 --threads \${GALAXY_SLOTS:-1} |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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33 ]]></command> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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34 <inputs> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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35 <expand macro="rank_taxon"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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36 <expand macro="bin_inputs"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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37 <section name="analyze" title="Marker gene identification"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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38 <expand macro="analyze_params" /> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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39 </section> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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40 <section name="qa" title="Bin assessment"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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41 <expand macro="qa_params" /> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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42 </section> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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43 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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44 <option value="marker_file">Marker genes</option> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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45 <option value="hmmer_analyze">Marker gene HMM hits to each bin</option> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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46 <option value="bin_stats_analyze">Marker gene bin stats</option> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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47 <option value="checkm_hmm_info">Marker gene HMM info for each bin</option> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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48 <expand macro="analyze_extra_output_options" /> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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49 <option value="bin_stats_ext">Marker gene bin extensive stats</option> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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50 <expand macro="qa_extra_output_options" /> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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51 </param> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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52 </inputs> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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53 <outputs> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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54 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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55 <!-- taxon_set outputs --> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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56 <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes"> |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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57 <filter>extra_outputs and 'marker_file' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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58 </data> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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59 <!--analyze outputs--> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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60 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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61 <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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62 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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63 </collection> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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64 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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65 <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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66 </data> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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67 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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68 <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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69 </data> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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70 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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71 <filter>analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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72 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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73 </collection> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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74 <!--qa outputs--> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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75 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> |
1
2e995a9aa00e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents:
0
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76 <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter> |
0
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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77 </data> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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78 <expand macro="qa_extra_outputs" /> |
91230b9141c1
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iuc
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79 </outputs> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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80 <tests> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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81 <test expect_num_outputs="1"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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82 <conditional name="bins"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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83 <param name="select" value="collection"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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84 <param name="bins_coll"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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85 <collection type="list"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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86 <element name="637000110" ftype="fasta" value="637000110.fna"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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87 </collection> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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88 </param> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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89 </conditional> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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90 <conditional name="rank_taxon"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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91 <param name="rank" value="life"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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92 <param name="taxon" value="Prokaryote"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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93 </conditional> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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94 <section name="analyze"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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95 <param name="ali" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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96 <param name="nt" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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97 <param name="genes" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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98 </section> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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99 <section name="qa"> |
91230b9141c1
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iuc
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100 <param name="individual_markers" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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101 <param name="skip_adj_correction" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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102 <param name="skip_pseudogene_correction" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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103 <param name="aai_strain" value="0.9"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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104 <param name="ignore_thresholds" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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105 <param name="e_value" value="1e-10"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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106 <param name="length" value="0.7"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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107 </section> |
91230b9141c1
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108 <param name="extra_outputs" value=""/> |
91230b9141c1
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109 <output name="results" ftype="tabular"> |
91230b9141c1
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110 <assert_contents> |
91230b9141c1
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iuc
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111 <has_text text="637000110"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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112 <has_text text="Marker lineage"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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113 <has_text text="Prokaryote"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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114 </assert_contents> |
91230b9141c1
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115 </output> |
91230b9141c1
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116 </test> |
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iuc
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117 <test expect_num_outputs="8"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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118 <conditional name="bins"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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119 <param name="select" value="collection"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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120 <param name="bins_coll"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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121 <collection type="list"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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122 <element name="637000110" ftype="fasta" value="637000110.fna"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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123 </collection> |
91230b9141c1
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124 </param> |
91230b9141c1
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iuc
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125 </conditional> |
91230b9141c1
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iuc
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126 <conditional name="rank_taxon"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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127 <param name="rank" value="life"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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128 <param name="taxon" value="Prokaryote"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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129 </conditional> |
91230b9141c1
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130 <section name="analyze"> |
91230b9141c1
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131 <param name="ali" value="true"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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132 <param name="nt" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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133 <param name="genes" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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134 </section> |
91230b9141c1
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135 <section name="qa"> |
91230b9141c1
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136 <param name="individual_markers" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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137 <param name="skip_adj_correction" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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138 <param name="skip_pseudogene_correction" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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139 <param name="aai_strain" value="0.9"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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140 <param name="ignore_thresholds" value="false"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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141 <param name="e_value" value="1e-10"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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142 <param name="length" value="0.7"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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143 </section> |
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144 <param name="extra_outputs" value="marker_file,hmmer_analyze,hmmer_analyze_ali,bin_stats_analyze,bin_stats_ext,checkm_hmm_info,marker_gene_stats"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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145 <output name="results" ftype="tabular"> |
91230b9141c1
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146 <assert_contents> |
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147 <has_text text="637000110"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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148 <has_text text="Marker lineage"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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149 <has_text text="Prokaryote"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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150 </assert_contents> |
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151 </output> |
91230b9141c1
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152 <output name="marker_file" ftype="tabular"> |
91230b9141c1
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153 <assert_contents> |
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154 <has_text text="[Taxon Marker File]"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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155 <has_text text="Prokaryote"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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156 <has_text text="PF01000.21"/> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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157 </assert_contents> |
91230b9141c1
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158 </output> |
91230b9141c1
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159 <output_collection name="hmmer_analyze" count="1"> |
91230b9141c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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160 <element name="637000110" ftype="txt"> |
91230b9141c1
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161 <assert_contents> |
91230b9141c1
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iuc
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162 <has_text text="target name"/> |
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163 <has_text text="AC_000091_570"/> |
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164 </assert_contents> |
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165 </element> |
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166 </output_collection> |
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167 <output name="bin_stats_analyze" ftype="tabular"> |
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168 <assert_contents> |
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169 <has_text text="637000110"/> |
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170 <has_text text="GC"/> |
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171 <has_text text="GC std"/> |
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172 </assert_contents> |
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173 </output> |
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174 <output name="checkm_hmm_info" ftype="zip"> |
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175 <assert_contents> |
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176 <has_size value="4373" delta="100"/> |
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177 </assert_contents> |
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178 </output> |
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179 <output_collection name="hmmer_analyze_ali" count="1"> |
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180 <element name="637000110" ftype="txt"> |
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181 <assert_contents> |
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182 <has_text text="hmmsearch"/> |
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183 <has_text text="Query"/> |
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184 <has_text text="TOBE_2"/> |
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185 </assert_contents> |
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186 </element> |
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187 </output_collection> |
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188 <output name="bin_stats_ext" ftype="tabular"> |
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189 <assert_contents> |
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190 <has_text text="637000110"/> |
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191 <has_text text="marker lineage"/> |
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192 </assert_contents> |
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193 </output> |
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194 <output name="marker_gene_stats" ftype="tabular"> |
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195 <assert_contents> |
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196 <has_text text="637000110"/> |
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197 <has_text text="AC_000091_79"/> |
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198 <has_text text="PF00318.15"/> |
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199 </assert_contents> |
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200 </output> |
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201 </test> |
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202 </tests> |
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203 <help><![CDATA[ |
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204 @HELP_HEADER@ |
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205 |
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206 This command runs recommended workflow to analyze all genome bins with the same marker set. A common example would be a set of genomes from the same taxonomic group. |
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207 |
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208 The workflow for using a taxonomic-specific marker set consists of 3 mandatory (M) steps and 1 recommended (R) step: |
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209 |
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210 - (R) The taxon_list command produces a table indicating all taxa for which a marker set can be produced. All support taxa at a given taxonomic rank can be produced by passing taxon_list the --rank flag |
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211 - (M) The taxon_set command is used to produce marker sets for a specific taxon: |
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212 - (M) The analyze command identifies marker genes within each genome bin and estimate completeness and contamination. All putative genomes to be analyzed must be provided. |
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213 - (M) The qa command is used to produce different tables summarizing the quality of each genome bin. |
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214 |
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215 Inputs |
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216 ====== |
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217 |
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218 |
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219 Outputs |
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220 ======= |
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221 |
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222 ]]></help> |
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223 <expand macro="citations"/> |
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224 </tool> |