Mercurial > repos > iuc > checkm_tree_qa

annotate tree_qa.xml @ 1:b9a38ce53252 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
author iuc
date Mon, 08 Aug 2022 20:00:26 +0000
parents dd51f61c2309
children
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dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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1 <tool id="checkm_tree_qa" name="CheckM tree_qa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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2 <description>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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3 Assess phylogenetic markers in the genome tree
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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4 </description>
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5 <macros>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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6 <import>macros.xml</import>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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7 <xml name="concatenated_tre">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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8 <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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9 </xml>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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10 </macros>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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11 <expand macro="biotools"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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12 <expand macro="requirements"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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13 <expand macro="version"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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14 <command detect_errors="exit_code"><![CDATA[
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15 @HMM_MARKER_STATS_INPUTS@
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16 mkdir 'inputs/storage/tree/' &&
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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17 #if $output.out_format != '5'
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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18 ln -s '$output.concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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19 #else
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20 ln -s '$output.concatenated_fasta' 'inputs/storage/tree/concatenated.fasta' &&
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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21 #end if
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22
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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23 checkm tree_qa
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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24 'inputs'
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 --out_format $output.out_format
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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26 --tab_table
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27 --file 'output_file'
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28 ]]></command>
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29 <inputs>
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30 <expand macro="hmm_marker_stats_inputs"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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31 <conditional name="output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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32 <param argument="--out_format" type="select" label="Desired output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 <option value="1">Brief summary of genome tree placement</option>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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34 <option value="2">Detailed summary of genome tree placement including lineage-specific statistics</option>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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35 <option value="3">Genome tree in Newick format decorated with IMG genome ids</option>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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36 <option value="4">Genome tree in Newick format decorated with taxonomy strings</option>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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37 <option value="5">Multiple sequence alignment of reference genomes and bins</option>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 <when value="1">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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40 <expand macro="concatenated_tre"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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41 </when>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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42 <when value="2">
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43 <expand macro="concatenated_tre"/>
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44 </when>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 <when value="3">
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46 <expand macro="concatenated_tre"/>
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47 </when>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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48 <when value="4">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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49 <expand macro="concatenated_tre"/>
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50 </when>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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51 <when value="5">
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52 <param name="concatenated_fasta" type="data" format="phyloxml" label="Concatenated masked sequences"/>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data name="output_f1" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Summary of genome tree placement">
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58 <filter>output['out_format']=="1"</filter>
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59 </data>
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60 <data name="output_f2" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Summary of genome tree placement including lineage-specific statistics">
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61 <filter>output['out_format']=="2"</filter>
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62 </data>
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63 <data name="output_f3" format="newick" from_work_dir="output_file" label="${tool.name} on ${on_string}: Genome tree decorated with IMG genome ids">
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64 <filter>output['out_format']=="3"</filter>
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65 </data>
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66 <data name="output_f4" format="newick" from_work_dir="output_file" label="${tool.name} on ${on_string}: Genome tree decorated with taxonomy strings">
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67 <filter>output['out_format']=="4"</filter>
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68 </data>
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69 <data name="output_f5" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Multiple sequence alignment of reference genomes and bins">
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70 <filter>output['out_format']=="5"</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test expect_num_outputs="1">
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75 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
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76 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
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77 <param name="hmmer_tree">
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78 <collection type="list">
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79 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
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80 </collection>
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81 </param>
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82 <conditional name="output">
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83 <param name="out_format" value="1"/>
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84 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
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85 </conditional>
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86 <output name="output_f1" ftype="tabular">
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87 <assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
88 <has_text text="637000110"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
89 <has_text text="k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
90 <has_text text="# unique markers"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
91 </assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
92 </output>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
93 </test>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
94 <test expect_num_outputs="1">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
95 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
96 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
97 <param name="hmmer_tree">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
98 <collection type="list">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
99 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
100 </collection>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
101 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
102 <conditional name="output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
103 <param name="out_format" value="2"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
104 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
105 </conditional>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
106 <output name="output_f2" ftype="tabular">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
107 <assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
108 <has_text text="637000110"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
109 <has_text text="# unique markers (of 43)"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
110 <has_text text="UID5220"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
111 </assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
112 </output>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
113 </test>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
114 <test expect_num_outputs="1">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
115 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
116 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
117 <param name="hmmer_tree">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
118 <collection type="list">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
119 <element name="IMG_646564547" ftype="txt" value="hmmer.tree.txt"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
120 </collection>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
121 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
122 <conditional name="output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
123 <param name="out_format" value="3"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
124 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
125 </conditional>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
126 <output name="output_f3" ftype="newick">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
127 <assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
128 <has_text text="IMG_646564547"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
129 <has_text text="UID7|f__Methanocaldococcaceae"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
130 <has_text text="f__Archaeoglobaceae"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
131 </assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
132 </output>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
133 </test>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
134 <test expect_num_outputs="1">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
135 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
136 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
137 <param name="hmmer_tree">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
138 <collection type="list">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
139 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
140 </collection>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
141 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
142 <conditional name="output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
143 <param name="out_format" value="4"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
144 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
145 </conditional>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
146 <output name="output_f4" ftype="newick">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
147 <assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
148 <has_text text="IMG_646564547"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
149 <has_text text="k__Archaea;p__Euryarchaeota"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
150 </assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
151 </output>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
152 </test>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
153 <test expect_num_outputs="1">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
154 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
155 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
156 <param name="hmmer_tree">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
157 <collection type="list">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
158 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
159 </collection>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
160 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
161 <conditional name="output">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
162 <param name="out_format" value="5"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
163 <param name="concatenated_fasta" ftype="fasta" value="concatenated.fasta"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
164 </conditional>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
165 <output name="output_f5" ftype="tabular">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
166 <assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
167 <has_text text=">637000110"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
168 <has_text text="-TVNQLVR"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
169 </assert_contents>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
170 </output>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
171 </test>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
172 </tests>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
173 <help><![CDATA[
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
174 @HELP_HEADER@
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
175
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
176 This command assesses phylogenetic markers in the genome tree
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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177
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178 Inputs
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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179 ======
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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180
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181
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182 Outputs
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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183 =======
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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184
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185 Output in function of selection output format
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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186
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187 1. brief summary of genome tree placement indicating the number of unique phylogenetically informative markers found, the number of markers found multiple times, and a taxon string indicating the placement of each bin within the genome tree
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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188 2. detailed summary of genome tree placement giving a more detailed indication of where each bin is within the genome tree, general characteristics about each bin (e.g., GC, genome size, coding density), and general characteristics about all reference genomes descendant from the parental node of each bin (e.g., mean and standard deviation of GC)
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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189 3. genome tree in Newick format decorated with IMG genome ids which can be used to examine the phylogenetic neighbours of each bin
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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190 4. genome tree in Newick format decorated with taxonomy strings which can be used to examine the phylogenetic neighbours of each bin
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191 5. multiple sequence alignment of reference genomes and bins which can be used to infer a de novo genome tree
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192
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193
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194 ]]></help>
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195 <expand macro="citations"/>
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196 </tool>