| Previous changeset 0:65c80ca30373 (2021-05-12) Next changeset 2:2cd76b089570 (2023-02-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 948cdafe28ae232b641a58bb7dc044d320feb294" |
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modified:
humann.xml macros.xml |
| b |
| diff -r 65c80ca30373 -r 6b7622dda516 humann.xml --- a/humann.xml Wed May 12 09:06:30 2021 +0000 +++ b/humann.xml Wed May 19 17:03:51 2021 +0000 |
| [ |
| b'@@ -150,7 +150,7 @@\n --search-mode \'$wf.translated_search.protein_db.search_mode\'\n #else\n --protein-database \'$wf.translated_search.protein_db.protein_database.fields.path\'\n- #if \'uniref50\' in $wf.translated_search.protein_db.protein_database.fields.dbkey\n+ #if \'uniref50\' in $wf.translated_search.protein_db.protein_database.fields.value\n --search-mode \'uniref50\'\n #else\n --search-mode \'uniref90\'\n@@ -261,7 +261,9 @@\n <option value="abundance">Pre-computed (typically gene) abundance tables</option>\n </param>\n <when value="raw">\n- <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Paired-end Fasta/FastQ files should be merged first"/>\n+ <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" \n+ label="Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))" \n+ help="Paired-end Fasta/FastQ files should be merged first"/>\n </when>\n <when value="mapping">\n <param name="input" type="data" format="sam,bam" label="Pre-computed mappings of reads to database sequences"/>\n@@ -273,7 +275,7 @@\n <conditional name="wf">\n <param name="selector" type="select" label="Steps">\n <option value="bypass_prescreen">Bypass the prescreen step and run on the full ChocoPhlAn database (--bypass-prescreen)</option>\n- <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species</option>\n+ <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species provided afterwards</option>\n <option value="bypass_nucleotide_index">Starts the workflow with the nucleotide alignment step using the provided indexed database (--bypass-nucleotide-index)</option>\n <option value="bypass_nucleotide_search">Bypass all of the alignment steps before the translated search (--bypass_nucleotide-search)</option>\n <option value="bypass_translated_search">Run all of the alignment steps except the translated search (--bypass_translated-search)</option>\n@@ -284,7 +286,7 @@\n <expand macro="translated_search"/>\n </when>\n <when value="bypass_taxonomic_profiling">\n- <param argument="--taxonomic-profile" type="data" format="tabular,txt" label="Taxonomic profile file"/>\n+ <param argument="--taxonomic-profile" type="data" format="tabular,txt,tsv" label="Taxonomic profile file"/>\n <expand macro="nucleotide_search"/>\n <expand macro="translated_search"/>\n </when>\n@@ -346,48 +348,48 @@\n </section>\n </inputs>\n <outputs>\n- <data format="tabular" name="gene_families_tsv" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >\n+ <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >\n <filter>out[\'output_format\'] == "tsv"</filter>\n </data>\n- <data format="biom1" name="gene_families_biom" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >\n+ <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >\n <filter>out[\'output_format\'] == "biom"</filter>\n </data>\n- <data format="tabular" name="pathcoverage_tsv" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways '..b't" from_work_dir="output/*_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >\n+ <filter>out[\'intermediate_temp\'] and "bowtie2_reduced_alignment" in out[\'intermediate_temp\']</filter>\n </data>\n- <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_humann_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >\n- <filter>"bowtie2_unaligned" in out[\'intermediate_temp\']</filter>\n+ <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >\n+ <filter>out[\'intermediate_temp\'] and "bowtie2_unaligned" in out[\'intermediate_temp\']</filter>\n </data>\n- <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_humann_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >\n- <filter>"custom_chocophlan_database" in out[\'intermediate_temp\']</filter>\n+ <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >\n+ <filter>out[\'intermediate_temp\'] and "custom_chocophlan_database" in out[\'intermediate_temp\']</filter>\n </data>\n- <data format="tabular" name="diamond_aligned" from_work_dir="output/*_humann_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >\n- <filter>"diamond_aligned" in out[\'intermediate_temp\']</filter>\n+ <data format="tabular" name="diamond_aligned" from_work_dir="output/*_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >\n+ <filter>out[\'intermediate_temp\'] and "diamond_aligned" in out[\'intermediate_temp\']</filter>\n </data>\n- <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_humann_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >\n- <filter>"diamond_unaligned" in out[\'intermediate_temp\']</filter>\n+ <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >\n+ <filter>out[\'intermediate_temp\'] and "diamond_unaligned" in out[\'intermediate_temp\']</filter>\n </data>\n </outputs>\n <tests>\n@@ -591,7 +593,7 @@\n </section>\n <output name="gene_families_biom" ftype="biom1">\n <assert_contents>\n- <has_text text="http://biom-format.org"/>\n+ <has_text text="biom-format"/>\n <has_text text="UniRef90_A0A396BPQ7|g__Bacteroides.s__Bacteroides_vulgatus"/>\n <has_text text="UniRef90_W8YTG4|unclassified"/>\n </assert_contents>\n@@ -600,7 +602,7 @@\n <assert_contents>\n <has_text text="TREE"/>\n <has_text text="format-url"/>\n- <has_text text="http://biom-format.org"/>\n+ <has_text text="biom-format"/>\n <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>\n <has_text text="humann_Coverage"/>\n </assert_contents>\n@@ -609,7 +611,7 @@\n <assert_contents>\n <has_text text="TREE"/>\n <has_text text="format-url"/>\n- <has_text text="http://biom-format.org"/>\n+ <has_text text="biom-format"/>\n <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>\n <has_text text="humann_Abundance"/>\n </assert_contents>\n' |
| b |
| diff -r 65c80ca30373 -r 6b7622dda516 macros.xml --- a/macros.xml Wed May 12 09:06:30 2021 +0000 +++ b/macros.xml Wed May 19 17:03:51 2021 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">3.0.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.01</token> <xml name="edam_ontology"> <edam_topics> |