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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
author | iuc |
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date | Mon, 08 Aug 2022 20:01:28 +0000 |
parents | 91230b9141c1 |
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<tool id="checkm_taxonomy_wf" name="CheckM taxonomy_wf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> Analyze all genome bins with the same marker set </description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ @BIN_INPUTS@ checkm taxonomy_wf '$rank_taxon.rank' '$rank_taxon.taxon.fields.value' 'bins' 'output' $analyze.ali $analyze.nt $analyze.genes $qa.individual_markers $qa.skip_adj_correction $qa.skip_pseudogene_correction --aai_strain $qa.aai_strain $qa.ignore_thresholds --e_value $qa.e_value --length $qa.length --file '$results' --tab_table --extension 'fasta' --threads \${GALAXY_SLOTS:-1} ]]></command> <inputs> <expand macro="rank_taxon"/> <expand macro="bin_inputs"/> <section name="analyze" title="Marker gene identification"> <expand macro="analyze_params" /> </section> <section name="qa" title="Bin assessment"> <expand macro="qa_params" /> </section> <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs"> <option value="marker_file">Marker genes</option> <option value="hmmer_analyze">Marker gene HMM hits to each bin</option> <option value="bin_stats_analyze">Marker gene bin stats</option> <option value="checkm_hmm_info">Marker gene HMM info for each bin</option> <expand macro="analyze_extra_output_options" /> <option value="bin_stats_ext">Marker gene bin extensive stats</option> <expand macro="qa_extra_output_options" /> </param> </inputs> <outputs> <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> <!-- taxon_set outputs --> <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes"> <filter>extra_outputs and 'marker_file' in extra_outputs</filter> </data> <!--analyze outputs--> <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter> <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> </collection> <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter> </data> <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter> </data> <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> <filter>analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter> <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> </collection> <!--qa outputs--> <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter> </data> <expand macro="qa_extra_outputs" /> <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics"> <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <conditional name="bins"> <param name="select" value="collection"/> <param name="bins_coll"> <collection type="list"> <element name="637000110" ftype="fasta" value="637000110.fna"/> </collection> </param> </conditional> <conditional name="rank_taxon"> <param name="rank" value="life"/> <param name="taxon" value="Prokaryote"/> </conditional> <section name="analyze"> <param name="ali" value="false"/> <param name="nt" value="false"/> <param name="genes" value="false"/> </section> <section name="qa"> <param name="individual_markers" value="false"/> <param name="skip_adj_correction" value="false"/> <param name="skip_pseudogene_correction" value="false"/> <param name="aai_strain" value="0.9"/> <param name="ignore_thresholds" value="false"/> <param name="e_value" value="1e-10"/> <param name="length" value="0.7"/> </section> <param name="extra_outputs" value=""/> <output name="results" ftype="tabular"> <assert_contents> <has_text text="637000110"/> <has_text text="Marker lineage"/> <has_text text="Prokaryote"/> </assert_contents> </output> </test> <test expect_num_outputs="8"> <conditional name="bins"> <param name="select" value="collection"/> <param name="bins_coll"> <collection type="list"> <element name="637000110" ftype="fasta" value="637000110.fna"/> </collection> </param> </conditional> <conditional name="rank_taxon"> <param name="rank" value="life"/> <param name="taxon" value="Prokaryote"/> </conditional> <section name="analyze"> <param name="ali" value="true"/> <param name="nt" value="false"/> <param name="genes" value="false"/> </section> <section name="qa"> <param name="individual_markers" value="false"/> <param name="skip_adj_correction" value="false"/> <param name="skip_pseudogene_correction" value="false"/> <param name="aai_strain" value="0.9"/> <param name="ignore_thresholds" value="false"/> <param name="e_value" value="1e-10"/> <param name="length" value="0.7"/> </section> <param name="extra_outputs" value="marker_file,hmmer_analyze,hmmer_analyze_ali,bin_stats_analyze,bin_stats_ext,checkm_hmm_info,marker_gene_stats"/> <output name="results" ftype="tabular"> <assert_contents> <has_text text="637000110"/> <has_text text="Marker lineage"/> <has_text text="Prokaryote"/> </assert_contents> </output> <output name="marker_file" ftype="tabular"> <assert_contents> <has_text text="[Taxon Marker File]"/> <has_text text="Prokaryote"/> <has_text text="PF01000.21"/> </assert_contents> </output> <output_collection name="hmmer_analyze" count="1"> <element name="637000110" ftype="txt"> <assert_contents> <has_text text="target name"/> <has_text text="AC_000091_570"/> </assert_contents> </element> </output_collection> <output name="bin_stats_analyze" ftype="tabular"> <assert_contents> <has_text text="637000110"/> <has_text text="GC"/> <has_text text="GC std"/> </assert_contents> </output> <output name="checkm_hmm_info" ftype="zip"> <assert_contents> <has_size value="4373" delta="100"/> </assert_contents> </output> <output_collection name="hmmer_analyze_ali" count="1"> <element name="637000110" ftype="txt"> <assert_contents> <has_text text="hmmsearch"/> <has_text text="Query"/> <has_text text="TOBE_2"/> </assert_contents> </element> </output_collection> <output name="bin_stats_ext" ftype="tabular"> <assert_contents> <has_text text="637000110"/> <has_text text="marker lineage"/> </assert_contents> </output> <output name="marker_gene_stats" ftype="tabular"> <assert_contents> <has_text text="637000110"/> <has_text text="AC_000091_79"/> <has_text text="PF00318.15"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ 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. The workflow for using a taxonomic-specific marker set consists of 3 mandatory (M) steps and 1 recommended (R) step: - (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 - (M) The taxon_set command is used to produce marker sets for a specific taxon: - (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. - (M) The qa command is used to produce different tables summarizing the quality of each genome bin. Inputs ====== Outputs ======= ]]></help> <expand macro="citations"/> </tool>