Mercurial > repos > iuc > humann
changeset 1:6b7622dda516 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 948cdafe28ae232b641a58bb7dc044d320feb294"
| author | iuc |
|---|---|
| date | Wed, 19 May 2021 17:03:51 +0000 |
| parents | 65c80ca30373 |
| children | 2cd76b089570 |
| files | humann.xml macros.xml |
| diffstat | 2 files changed, 32 insertions(+), 30 deletions(-) [+] |
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--- a/humann.xml Wed May 12 09:06:30 2021 +0000 +++ b/humann.xml Wed May 19 17:03:51 2021 +0000 @@ -150,7 +150,7 @@ --search-mode '$wf.translated_search.protein_db.search_mode' #else --protein-database '$wf.translated_search.protein_db.protein_database.fields.path' - #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.dbkey + #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value --search-mode 'uniref50' #else --search-mode 'uniref90' @@ -261,7 +261,9 @@ <option value="abundance">Pre-computed (typically gene) abundance tables</option> </param> <when value="raw"> - <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Paired-end Fasta/FastQ files should be merged first"/> + <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" + label="Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))" + help="Paired-end Fasta/FastQ files should be merged first"/> </when> <when value="mapping"> <param name="input" type="data" format="sam,bam" label="Pre-computed mappings of reads to database sequences"/> @@ -273,7 +275,7 @@ <conditional name="wf"> <param name="selector" type="select" label="Steps"> <option value="bypass_prescreen">Bypass the prescreen step and run on the full ChocoPhlAn database (--bypass-prescreen)</option> - <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species</option> + <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species provided afterwards</option> <option value="bypass_nucleotide_index">Starts the workflow with the nucleotide alignment step using the provided indexed database (--bypass-nucleotide-index)</option> <option value="bypass_nucleotide_search">Bypass all of the alignment steps before the translated search (--bypass_nucleotide-search)</option> <option value="bypass_translated_search">Run all of the alignment steps except the translated search (--bypass_translated-search)</option> @@ -284,7 +286,7 @@ <expand macro="translated_search"/> </when> <when value="bypass_taxonomic_profiling"> - <param argument="--taxonomic-profile" type="data" format="tabular,txt" label="Taxonomic profile file"/> + <param argument="--taxonomic-profile" type="data" format="tabular,txt,tsv" label="Taxonomic profile file"/> <expand macro="nucleotide_search"/> <expand macro="translated_search"/> </when> @@ -346,48 +348,48 @@ </section> </inputs> <outputs> - <data format="tabular" name="gene_families_tsv" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" > + <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" > <filter>out['output_format'] == "tsv"</filter> </data> - <data format="biom1" name="gene_families_biom" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" > + <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" > <filter>out['output_format'] == "biom"</filter> </data> - <data format="tabular" name="pathcoverage_tsv" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" > + <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" > <filter>out['output_format'] == "tsv"</filter> </data> - <data format="biom1" name="pathcoverage_biom" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" > + <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" > <filter>out['output_format'] == "biom"</filter> </data> - <data format="tabular" name="pathabundance_tsv" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" > + <data name="pathabundance_tsv" format="tabular" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" > <filter>out['output_format'] == "tsv"</filter> </data> - <data format="biom1" name="pathabundance_biom" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" > + <data name="pathabundance_biom" format="biom1" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" > <filter>out['output_format'] == "biom"</filter> </data> <data format="txt" name="log" label="${tool.name} on ${on_string}: Log"/> - <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/*_humann_temp/*_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" > - <filter>"metaphlan_bowtie2" in out['intermediate_temp']</filter> + <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/*_temp/*_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" > + <filter>out['intermediate_temp'] and "metaphlan_bowtie2" in out['intermediate_temp']</filter> </data> - <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_humann_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" > - <filter>"metaphlan_bugs_list" in out['intermediate_temp']</filter> + <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" > + <filter>out['intermediate_temp'] and "metaphlan_bugs_list" in out['intermediate_temp']</filter> </data> - <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" > - <filter>"bowtie2_alignment" in out['intermediate_temp']</filter> + <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" > + <filter>out['intermediate_temp'] and "bowtie2_alignment" in out['intermediate_temp']</filter> </data> - <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" > - <filter>"bowtie2_reduced_alignment" in out['intermediate_temp']</filter> + <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" > + <filter>out['intermediate_temp'] and "bowtie2_reduced_alignment" in out['intermediate_temp']</filter> </data> - <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_humann_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" > - <filter>"bowtie2_unaligned" in out['intermediate_temp']</filter> + <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" > + <filter>out['intermediate_temp'] and "bowtie2_unaligned" in out['intermediate_temp']</filter> </data> - <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_humann_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" > - <filter>"custom_chocophlan_database" in out['intermediate_temp']</filter> + <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" > + <filter>out['intermediate_temp'] and "custom_chocophlan_database" in out['intermediate_temp']</filter> </data> - <data format="tabular" name="diamond_aligned" from_work_dir="output/*_humann_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" > - <filter>"diamond_aligned" in out['intermediate_temp']</filter> + <data format="tabular" name="diamond_aligned" from_work_dir="output/*_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" > + <filter>out['intermediate_temp'] and "diamond_aligned" in out['intermediate_temp']</filter> </data> - <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_humann_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" > - <filter>"diamond_unaligned" in out['intermediate_temp']</filter> + <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" > + <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter> </data> </outputs> <tests> @@ -591,7 +593,7 @@ </section> <output name="gene_families_biom" ftype="biom1"> <assert_contents> - <has_text text="http://biom-format.org"/> + <has_text text="biom-format"/> <has_text text="UniRef90_A0A396BPQ7|g__Bacteroides.s__Bacteroides_vulgatus"/> <has_text text="UniRef90_W8YTG4|unclassified"/> </assert_contents> @@ -600,7 +602,7 @@ <assert_contents> <has_text text="TREE"/> <has_text text="format-url"/> - <has_text text="http://biom-format.org"/> + <has_text text="biom-format"/> <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> <has_text text="humann_Coverage"/> </assert_contents> @@ -609,7 +611,7 @@ <assert_contents> <has_text text="TREE"/> <has_text text="format-url"/> - <has_text text="http://biom-format.org"/> + <has_text text="biom-format"/> <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> <has_text text="humann_Abundance"/> </assert_contents>
--- a/macros.xml Wed May 12 09:06:30 2021 +0000 +++ b/macros.xml Wed May 19 17:03:51 2021 +0000 @@ -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>