Mercurial > repos > iuc > checkm_lineage_wf

annotate lineage_wf.xml @ 2:8345d273ba82 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
author iuc
date Mon, 02 Sep 2024 13:50:15 +0000
parents f0107b9f2dc3
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760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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1 <tool id="checkm_lineage_wf" name="CheckM lineage_wf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Assessing the completeness and contamination of genome bins using lineage-specific marker sets
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @BIN_INPUTS@
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13
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14 checkm lineage_wf
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15 'bins'
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16 'output'
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17 $tree_analyze.reduced_tree
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18 $tree_analyze.ali
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19 $tree_analyze.nt
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20 $tree_analyze.genes
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21 --unique '$lineage_set.unique'
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22 --multi '$lineage_set.multi'
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23 $lineage_set.force_domain
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24 $lineage_set.no_refinement
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25 $qa.individual_markers
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26 $qa.skip_adj_correction
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27 $qa.skip_pseudogene_correction
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28 --aai_strain $qa.aai_strain
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29 $qa.ignore_thresholds
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30 --e_value $qa.e_value
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31 --length $qa.length
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32 --file '$results'
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33 --tab_table
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34 --extension 'fasta'
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35 --threads \${GALAXY_SLOTS:-1}
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36 --pplacer_threads \${GALAXY_SLOTS:-1}
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37 ]]></command>
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38 <inputs>
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39 <expand macro="bin_inputs" />
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40 <section name="tree_analyze" title="Bin placement in the genome tree and marker gene identification">
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41 <expand macro="tree_params" />
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42 </section>
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43 <section name="lineage_set" title="Bin lineage-specific marker set inference">
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44 <expand macro="lineage_set_params" />
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45 </section>
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46 <section name="qa" title="Bin assessment">
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47 <expand macro="qa_params" />
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48 </section>
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49 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
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50 <option value="phylo_hmm_info">Phylogenetic HMM model info for each bin</option>
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51 <option value="bin_stats_tree">Phylogenetic bin stats</option>
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52 <option value="hmmer_tree">Phylogenetic HMM hits to each bin</option>
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53 <option value="concatenated_tre">Concatenated tree</option>
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54 <option value="concatenated_fasta">Concatenated masked sequences</option>
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55 <expand macro="tree_extra_output_options" />
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56 <option value="marker_file">Marker genes</option>
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57 <option value="hmmer_analyze">Marker gene HMM hits to each bin</option>
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58 <option value="bin_stats_analyze">Marker gene bin stats</option>
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59 <option value="checkm_hmm_info">Marker gene HMM info for each bin</option>
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60 <expand macro="analyze_extra_output_options" />
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61 <option value="bin_stats_ext">Marker gene bin extensive stats</option>
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62 <expand macro="qa_extra_output_options" />
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63 </param>
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64 </inputs>
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65 <outputs>
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66 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/>
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67 <!--tree outputs-->
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68 <data name="phylo_hmm_info" format="zip" from_work_dir="output/storage/phylo_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Phylogenetic HMM model info for each bin">
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69 <filter>extra_outputs and 'phylo_hmm_info' in extra_outputs</filter>
0
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70 </data>
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71 <data name="bin_stats_tree" format="tabular" from_work_dir="output/storage/bin_stats.tree.tsv" label="${tool.name} on ${on_string}: Phylogenetic bin stats">
1
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72 <filter>extra_outputs and 'bin_stats_tree' in extra_outputs</filter>
0
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73 </data>
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74 <collection name="hmmer_tree" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMM hits to each bin">
1
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75 <filter>extra_outputs and 'hmmer_tree' in extra_outputs</filter>
0
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76 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
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77 </collection>
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78 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences">
1
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79 <filter>extra_outputs and 'concatenated_fasta' in extra_outputs</filter>
0
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80 </data>
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81 <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree">
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82 <filter>extra_outputs and 'concatenated_tre' in extra_outputs</filter>
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83 </data>
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84 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin">
1
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iuc
parents: 0
diff changeset
85 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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86 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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diff changeset
87 </collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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88 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
diff changeset
89 <filter>extra_outputs and 'concatenate_pplacer_json' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
90 </data>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
91 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
diff changeset
92 <filter>not tree_analyze['genes'] and tree_analyze['nt'] and extra_outputs and 'genes_fna' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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93 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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94 </collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
95 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
diff changeset
96 <filter>extra_outputs and 'genes_faa' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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97 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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98 </collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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diff changeset
99 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
diff changeset
100 <filter>not tree_analyze['genes'] and extra_outputs and 'genes_gff' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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101 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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102 </collection>
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103 <!--lineage_set outputs-->
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104 <data name="marker_file" format="tabular" from_work_dir="output/lineage.ms" label="${tool.name} on ${on_string}: Marker genes">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
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105 <filter>extra_outputs and 'marker_file' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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106 </data>
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107 <!--analyze outputs-->
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108 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
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parents: 0
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109 <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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110 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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111 </collection>
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112 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
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113 <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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114 </data>
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115 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" >
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
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116 <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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117 </data>
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118 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
diff changeset
119 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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120 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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121 </collection>
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122 <!--qa outputs-->
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123 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats">
1
f0107b9f2dc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
iuc
parents: 0
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124 <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter>
0
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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125 </data>
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126 <expand macro="qa_extra_outputs" />
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127 </outputs>
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128 <tests>
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129 <test expect_num_outputs="1">
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130 <conditional name="bins">
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131 <param name="select" value="individual"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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132 <param name="bins_ind" ftype="fasta" value="637000110.fna"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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133 </conditional>
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iuc
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134 <section name="tree_analyze">
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135 <param name="reduced_tree" value="true"/>
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136 <param name="ali" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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137 <param name="nt" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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138 <param name="genes" value="false"/>
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139 </section>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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140 <section name="lineage_set">
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141 <param name="unique" value="10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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142 <param name="multi" value="10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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143 <param name="force_domain" value="false"/>
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144 <param name="no_refinement" value="false"/>
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145 </section>
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146 <section name="qa">
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147 <param name="individual_markers" value="false"/>
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148 <param name="skip_adj_correction" value="false"/>
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149 <param name="skip_pseudogene_correction" value="false"/>
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150 <param name="aai_strain" value="0.9"/>
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151 <param name="ignore_thresholds" value="false"/>
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152 <param name="e_value" value="1e-10"/>
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153 <param name="length" value="0.7"/>
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154 </section>
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155 <param name="extra_outputs" value=""/>
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156 <output name="results" ftype="tabular">
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157 <assert_contents>
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158 <has_text text="637000110"/>
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159 <has_text text="Marker lineage"/>
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160 <has_text text="k__Bacteria"/>
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161 </assert_contents>
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162 </output>
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163 </test>
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164 <test expect_num_outputs="12">
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165 <conditional name="bins">
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166 <param name="select" value="collection"/>
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167 <param name="bins_coll">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
168 <collection type="list">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
169 <element name="637000110" ftype="fasta" value="637000110.fna"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
170 </collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
171 </param>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
172 </conditional>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
173 <section name="tree_analyze">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
174 <param name="reduced_tree" value="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
175 <param name="ali" value="true"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
176 <param name="nt" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
177 <param name="genes" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
178 </section>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
179 <section name="lineage_set">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
180 <param name="unique" value="10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
181 <param name="multi" value="10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
182 <param name="force_domain" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
183 <param name="no_refinement" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
184 </section>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
185 <section name="qa">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
186 <param name="individual_markers" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
187 <param name="skip_adj_correction" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
188 <param name="skip_pseudogene_correction" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
189 <param name="aai_strain" value="0.9"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
190 <param name="ignore_thresholds" value="false"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
191 <param name="e_value" value="1e-10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
192 <param name="length" value="0.7"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
193 </section>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
194 <param name="extra_outputs" value="phylo_hmm_info,bin_stats_tree,hmmer_tree,concatenated_tre,concatenated_fasta,marker_file,hmmer_analyze,bin_stats_analyze,bin_stats_ext,checkm_hmm_info,marker_gene_stats"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
195 <output name="results" ftype="tabular">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
196 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
197 <has_text text="637000110"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
198 <has_text text="Marker lineage"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
199 <has_text text="k__Bacteria"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
200 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
201 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
202 <output name="phylo_hmm_info" ftype="zip">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
203 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
204 <has_size value="1575" delta="10"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
205 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
206 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
207 <output name="bin_stats_tree" ftype="tabular">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
208 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
209 <has_text text="637000110"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
210 <has_text text="Mean scaffold length"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
211 <has_text text="Translation table"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
212 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
213 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
214 <output_collection name="hmmer_tree" count="1">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
215 <element name="637000110" ftype="txt">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
216 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
217 <has_text text="target name"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
218 <has_text text="AC_000091_79"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
219 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
220 </element>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
221 </output_collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
222 <output name="concatenated_fasta" ftype="fasta">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
223 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
224 <has_text text="637000110"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
225 <has_text text="MLKAGVHFGHQ"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
226 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
227 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
228 <output name="concatenated_tre" ftype="phyloxml">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
229 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
230 <has_text text="IMG_646564547"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
231 <has_text text="g__Methanocaldococcus"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
232 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
233 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
234 <output name="marker_file" ftype="tabular">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
235 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
236 <has_text text="Lineage Marker File"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
237 <has_text text="637000110"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
238 <has_text text="k__Bacteria"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
239 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
240 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
241 <output_collection name="hmmer_analyze" count="1">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
242 <element name="637000110" ftype="txt">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
243 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
244 <has_text text="target name"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
245 <has_text text="AC_000091_859"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
246 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
247 </element>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
248 </output_collection>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
249 <output name="bin_stats_analyze" ftype="tabular">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
250 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
251 <has_text text="637000110"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
252 <has_text text="GC"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
253 <has_text text="GC std"/>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
254 </assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
255 </output>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
256 <output name="bin_stats_ext" ftype="tabular">
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
257 <assert_contents>
760dc0c0e689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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258 <has_text text="637000110"/>
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259 <has_text text="marker lineage"/>
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260 </assert_contents>
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261 </output>
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262 <output name="checkm_hmm_info" ftype="zip">
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263 <assert_contents>
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264 <has_size value="17052" delta="200"/>
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265 </assert_contents>
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266 </output>
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267 <output name="marker_gene_stats" ftype="tabular">
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268 <assert_contents>
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269 <has_text text="637000110"/>
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270 <has_text text="AC_000091_79"/>
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271 <has_text text="PF00318.15"/>
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272 </assert_contents>
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273 </output>
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274 </test>
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275 </tests>
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276 <help><![CDATA[
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277 @HELP_HEADER@
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278
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279 This command runs the recommended workflow for assessing the completeness and contamination of genome bins is to use lineage-specific marker sets.
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280 This workflow consists of 4 mandatory (M) steps and 1 recommended (R) step:
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281
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282 - (M) The tree command places genome bins into a reference genome tree
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283 - (R) The tree_qa command indicates the number of phylogenetically informative marker genes found in each genome bin along with a taxonomic string indicating its approximate placement in the tree.
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284
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285 If desired, genome bins with few phylogenetically marker genes may be removed in order to reduce the computational requirements of the following commands.
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286 Alternatively, if only genomes from a particular taxonomic group are of interest these can be moved to a new directory and analyzed separately.
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287
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288 - (M) The lineage_set command creates a marker file indicating lineage-specific marker sets suitable for evaluating each genome.
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289 - (M) The analyze command identifies marker genes and estimates the completeness and contamination of each genome bin.
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290 - (M) The qa command can be used to produce different tables summarizing the quality of each genome bin.
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291
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292 ]]></help>
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293 <expand macro="citations"/>
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294 </tool>