| Previous changeset 11:b6897977d13e (2024-07-29) Next changeset 13:ef65b083bd0c (2024-09-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb |
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modified:
metaphlan.xml |
| b |
| diff -r b6897977d13e -r 1a037928504c metaphlan.xml --- a/metaphlan.xml Mon Jul 29 07:14:21 2024 +0000 +++ b/metaphlan.xml Sun Aug 11 20:35:53 2024 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">\n <description>to profile the composition of microbial communities</description>\n <macros>\n <import>macros.xml</import>\n@@ -15,8 +15,7 @@\n <option value="s">Species only</option>\n </param>\n <when value="a">\n- <param name="split_levels" type=\'boolean\' checked="false" truevalue=\'true\' falsevalue=\'false\' \n- label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>\n+ <param name="split_levels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>\n </when>\n <when value="k"/>\n <when value="p"/>\n@@ -261,10 +260,10 @@\n <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>\n </when>\n <when value="multiple">\n- <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>\n+ <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ files with microbiota reads" multiple="true"/>\n </when>\n <when value="paired_collection">\n- <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads"/>\n+ <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads" collection_type="paired"/>\n </when>\n <when value="paired">\n <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>\n@@ -286,8 +285,7 @@\n <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>\n </when>\n <when value="bowtie2out">\n- <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" \n- help="File needs to be generated with MetaPhlAn versions >3.0"/>\n+ <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions >3.0"/>\n </when>\n </conditional>\n <conditional name="db">\n@@ -317,7 +315,7 @@\n <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>\n <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>\n <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>\n- <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>\n+ <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>\n <option value="marker_counts">marker_coun'..b' reads mapping to known clades in order to estimate unknowness?"/>\n+ <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/>\n </section>\n <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) -->\n <param name="test" type="hidden" value="false"/>\n </inputs>\n <outputs>\n- <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />\n+ <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/>\n <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">\n <filter>inputs[\'in\'][\'selector\'] == "raw"</filter>\n </data>\n <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">\n <filter>inputs[\'in\'][\'selector\'] == "raw"</filter>\n </data>\n- <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />\n- <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >\n+ <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/>\n+ <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels">\n <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/>\n <filter>analysis[\'analysis_type\'][\'t\'] in [\'rel_ab\', \'rel_ab_w_read_stats\'] and analysis[\'analysis_type\'][\'tax_lev\'][\'tax_lev\'] == "a" and analysis[\'analysis_type\'][\'tax_lev\'][\'split_levels\']</filter>\n </collection>\n@@ -654,7 +642,7 @@\n <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>\n </assert_contents>\n </output>\n- <output_collection name="levels" type="list" >\n+ <output_collection name="levels" type="list">\n <element name="all" ftype="tabular">\n <assert_contents>\n <has_text text="Gammaproteobacteria"/>\n@@ -896,7 +884,6 @@\n </assert_contents>\n </element>\n </output_collection>\n-\n <assert_stderr>\n <has_text text="Downloading" negate="true"/>\n </assert_stderr>\n@@ -992,7 +979,6 @@\n </assert_contents>\n </element>\n </output_collection>\n-\n <assert_stderr>\n <has_text text="Downloading" negate="true"/>\n </assert_stderr>\n@@ -1179,7 +1165,7 @@\n <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>\n </assert_contents>\n </output>\n- <output_collection name="levels" type="list" >\n+ <output_collection name="levels" type="list">\n <element name="all" ftype="tabular">\n <assert_contents>\n <has_text text="Gammaproteobacteria"/>\n@@ -1309,7 +1295,8 @@\n <has_text text="--vsc_out"/>\n </assert_command>\n <assert_stderr>\n- <has_text text="Downloading"/> <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->\n+ <has_text text="Downloading"/>\n+ <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->\n <has_text text="No reads aligning to VSC markers"/>\n </assert_stderr>\n </test>\n' |