Mercurial > repos > iuc > checkm_taxonomy_wf
comparison taxonomy_wf.xml @ 0:91230b9141c1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author | iuc |
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date | Fri, 29 Jul 2022 20:32:07 +0000 |
parents | |
children | 2e995a9aa00e |
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1 <tool id="checkm_taxonomy_wf" name="CheckM taxonomy_wf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description> | |
3 Analyze all genome bins with the same marker set | |
4 </description> | |
5 <macros> | |
6 <import>macros.xml</import> | |
7 </macros> | |
8 <expand macro="biotools"/> | |
9 <expand macro="requirements"/> | |
10 <expand macro="version"/> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 @BIN_INPUTS@ | |
13 | |
14 checkm taxonomy_wf | |
15 '$rank_taxon.rank' | |
16 '$rank_taxon.taxon.fields.value' | |
17 'bins' | |
18 'output' | |
19 $analyze.ali | |
20 $analyze.nt | |
21 $analyze.genes | |
22 $qa.individual_markers | |
23 $qa.skip_adj_correction | |
24 $qa.skip_pseudogene_correction | |
25 --aai_strain $qa.aai_strain | |
26 $qa.ignore_thresholds | |
27 --e_value $qa.e_value | |
28 --length $qa.length | |
29 --file '$results' | |
30 --tab_table | |
31 --extension 'fasta' | |
32 --threads \${GALAXY_SLOTS:-1} | |
33 ]]></command> | |
34 <inputs> | |
35 <expand macro="rank_taxon"/> | |
36 <expand macro="bin_inputs"/> | |
37 <section name="analyze" title="Marker gene identification"> | |
38 <expand macro="analyze_params" /> | |
39 </section> | |
40 <section name="qa" title="Bin assessment"> | |
41 <expand macro="qa_params" /> | |
42 </section> | |
43 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs"> | |
44 <option value="marker_file">Marker genes</option> | |
45 <option value="hmmer_analyze">Marker gene HMM hits to each bin</option> | |
46 <option value="bin_stats_analyze">Marker gene bin stats</option> | |
47 <option value="checkm_hmm_info">Marker gene HMM info for each bin</option> | |
48 <expand macro="analyze_extra_output_options" /> | |
49 <option value="bin_stats_ext">Marker gene bin extensive stats</option> | |
50 <expand macro="qa_extra_output_options" /> | |
51 </param> | |
52 </inputs> | |
53 <outputs> | |
54 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> | |
55 <!-- taxon_set outputs --> | |
56 <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes"> | |
57 <filter>'marker_file' in extra_outputs</filter> | |
58 </data> | |
59 <!--analyze outputs--> | |
60 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> | |
61 <filter>'hmmer_analyze' in extra_outputs</filter> | |
62 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | |
63 </collection> | |
64 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> | |
65 <filter>'bin_stats_analyze' in extra_outputs</filter> | |
66 </data> | |
67 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > | |
68 <filter>'checkm_hmm_info' in extra_outputs</filter> | |
69 </data> | |
70 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> | |
71 <filter>analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter> | |
72 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | |
73 </collection> | |
74 <!--qa outputs--> | |
75 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> | |
76 <filter>'bin_stats_ext' in extra_outputs</filter> | |
77 </data> | |
78 <expand macro="qa_extra_outputs" /> | |
79 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics"> | |
80 <filter>'marker_gene_stats' in extra_outputs</filter> | |
81 </data> | |
82 </outputs> | |
83 <tests> | |
84 <test expect_num_outputs="1"> | |
85 <conditional name="bins"> | |
86 <param name="select" value="collection"/> | |
87 <param name="bins_coll"> | |
88 <collection type="list"> | |
89 <element name="637000110" ftype="fasta" value="637000110.fna"/> | |
90 </collection> | |
91 </param> | |
92 </conditional> | |
93 <conditional name="rank_taxon"> | |
94 <param name="rank" value="life"/> | |
95 <param name="taxon" value="Prokaryote"/> | |
96 </conditional> | |
97 <section name="analyze"> | |
98 <param name="ali" value="false"/> | |
99 <param name="nt" value="false"/> | |
100 <param name="genes" value="false"/> | |
101 </section> | |
102 <section name="qa"> | |
103 <param name="individual_markers" value="false"/> | |
104 <param name="skip_adj_correction" value="false"/> | |
105 <param name="skip_pseudogene_correction" value="false"/> | |
106 <param name="aai_strain" value="0.9"/> | |
107 <param name="ignore_thresholds" value="false"/> | |
108 <param name="e_value" value="1e-10"/> | |
109 <param name="length" value="0.7"/> | |
110 </section> | |
111 <param name="extra_outputs" value=""/> | |
112 <output name="results" ftype="tabular"> | |
113 <assert_contents> | |
114 <has_text text="637000110"/> | |
115 <has_text text="Marker lineage"/> | |
116 <has_text text="Prokaryote"/> | |
117 </assert_contents> | |
118 </output> | |
119 </test> | |
120 <test expect_num_outputs="8"> | |
121 <conditional name="bins"> | |
122 <param name="select" value="collection"/> | |
123 <param name="bins_coll"> | |
124 <collection type="list"> | |
125 <element name="637000110" ftype="fasta" value="637000110.fna"/> | |
126 </collection> | |
127 </param> | |
128 </conditional> | |
129 <conditional name="rank_taxon"> | |
130 <param name="rank" value="life"/> | |
131 <param name="taxon" value="Prokaryote"/> | |
132 </conditional> | |
133 <section name="analyze"> | |
134 <param name="ali" value="true"/> | |
135 <param name="nt" value="false"/> | |
136 <param name="genes" value="false"/> | |
137 </section> | |
138 <section name="qa"> | |
139 <param name="individual_markers" value="false"/> | |
140 <param name="skip_adj_correction" value="false"/> | |
141 <param name="skip_pseudogene_correction" value="false"/> | |
142 <param name="aai_strain" value="0.9"/> | |
143 <param name="ignore_thresholds" value="false"/> | |
144 <param name="e_value" value="1e-10"/> | |
145 <param name="length" value="0.7"/> | |
146 </section> | |
147 <param name="extra_outputs" value="marker_file,hmmer_analyze,hmmer_analyze_ali,bin_stats_analyze,bin_stats_ext,checkm_hmm_info,marker_gene_stats"/> | |
148 <output name="results" ftype="tabular"> | |
149 <assert_contents> | |
150 <has_text text="637000110"/> | |
151 <has_text text="Marker lineage"/> | |
152 <has_text text="Prokaryote"/> | |
153 </assert_contents> | |
154 </output> | |
155 <output name="marker_file" ftype="tabular"> | |
156 <assert_contents> | |
157 <has_text text="[Taxon Marker File]"/> | |
158 <has_text text="Prokaryote"/> | |
159 <has_text text="PF01000.21"/> | |
160 </assert_contents> | |
161 </output> | |
162 <output_collection name="hmmer_analyze" count="1"> | |
163 <element name="637000110" ftype="txt"> | |
164 <assert_contents> | |
165 <has_text text="target name"/> | |
166 <has_text text="AC_000091_570"/> | |
167 </assert_contents> | |
168 </element> | |
169 </output_collection> | |
170 <output name="bin_stats_analyze" ftype="tabular"> | |
171 <assert_contents> | |
172 <has_text text="637000110"/> | |
173 <has_text text="GC"/> | |
174 <has_text text="GC std"/> | |
175 </assert_contents> | |
176 </output> | |
177 <output name="checkm_hmm_info" ftype="zip"> | |
178 <assert_contents> | |
179 <has_size value="4373" delta="100"/> | |
180 </assert_contents> | |
181 </output> | |
182 <output_collection name="hmmer_analyze_ali" count="1"> | |
183 <element name="637000110" ftype="txt"> | |
184 <assert_contents> | |
185 <has_text text="hmmsearch"/> | |
186 <has_text text="Query"/> | |
187 <has_text text="TOBE_2"/> | |
188 </assert_contents> | |
189 </element> | |
190 </output_collection> | |
191 <output name="bin_stats_ext" ftype="tabular"> | |
192 <assert_contents> | |
193 <has_text text="637000110"/> | |
194 <has_text text="marker lineage"/> | |
195 </assert_contents> | |
196 </output> | |
197 <output name="marker_gene_stats" ftype="tabular"> | |
198 <assert_contents> | |
199 <has_text text="637000110"/> | |
200 <has_text text="AC_000091_79"/> | |
201 <has_text text="PF00318.15"/> | |
202 </assert_contents> | |
203 </output> | |
204 </test> | |
205 </tests> | |
206 <help><![CDATA[ | |
207 @HELP_HEADER@ | |
208 | |
209 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. | |
210 | |
211 The workflow for using a taxonomic-specific marker set consists of 3 mandatory (M) steps and 1 recommended (R) step: | |
212 | |
213 - (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 | |
214 - (M) The taxon_set command is used to produce marker sets for a specific taxon: | |
215 - (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. | |
216 - (M) The qa command is used to produce different tables summarizing the quality of each genome bin. | |
217 | |
218 Inputs | |
219 ====== | |
220 | |
221 | |
222 Outputs | |
223 ======= | |
224 | |
225 ]]></help> | |
226 <expand macro="citations"/> | |
227 </tool> |