comparison humann.xml @ 1:6b7622dda516 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 948cdafe28ae232b641a58bb7dc044d320feb294"

0:65c80ca30373

            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$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
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if

                <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
                <option value="mapping">Pre-computed mappings of reads to database sequences</option>
                <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"/>
            </when>
            <when value="mapping">
                <param name="input" type="data" format="sam,bam" label="Pre-computed mappings of reads to database sequences"/>
            </when>
            <when value="abundance">

            </when>
        </conditional>
        <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_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>
                <option value="none" selected="true">Run the full workflow steps</option>
            </param>
            <when value="bypass_prescreen">
                <expand macro="nucleotide_search"/>
                <expand macro="translated_search"/>
            </when>
            <when value="bypass_taxonomic_profiling">
                <param argument="--taxonomic-profile" type="data" format="tabular,txt" label="Taxonomic profile file"/>
                <expand macro="nucleotide_search"/>
                <expand macro="translated_search"/>
            </when>
            <when value="bypass_nucleotide_index">
                <expand macro="nucleotide_search"/>

                <option value="diamond_unaligned">Translated alignment unaligned reads</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="gene_families_tsv" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data format="biom1" name="gene_families_biom" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
            <filter>out['output_format'] == "biom"</filter>
        </data>
        <data format="tabular" name="pathcoverage_tsv" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data format="biom1" name="pathcoverage_biom" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
            <filter>out['output_format'] == "biom"</filter>
        </data>
        <data format="tabular" name="pathabundance_tsv" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data format="biom1" name="pathabundance_biom" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" >
            <filter>out['output_format'] == "biom"</filter>
        </data>
        <data format="txt" name="log" label="${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 ${on_string}: MetaPhlAn Bowtie2 output" >
            <filter>"metaphlan_bowtie2" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_humann_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" >
            <filter>"metaphlan_bugs_list" in out['intermediate_temp']</filter>
        </data>
        <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" >
            <filter>"bowtie2_alignment" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >
            <filter>"bowtie2_reduced_alignment" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_humann_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >
            <filter>"bowtie2_unaligned" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_humann_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >
            <filter>"custom_chocophlan_database" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="diamond_aligned" from_work_dir="output/*_humann_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >
            <filter>"diamond_aligned" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_humann_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
            <filter>"diamond_unaligned" in out['intermediate_temp']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="12">
            <conditional name="in">

                <param name="remove_statified_output" value="false"/>
                <param name="intermediate_temp" value=""/>
            </section>
            <output name="gene_families_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="http://biom-format.org"/>
                    <has_text text="UniRef90_A0A396BPQ7|g__Bacteroides.s__Bacteroides_vulgatus"/>
                    <has_text text="UniRef90_W8YTG4|unclassified"/>
                </assert_contents>
            </output>
            <output name="pathcoverage_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="TREE"/>
                    <has_text text="format-url"/>
                    <has_text text="http://biom-format.org"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_text text="humann_Coverage"/>
                </assert_contents>
            </output>
            <output name="pathabundance_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="TREE"/>
                    <has_text text="format-url"/>
                    <has_text text="http://biom-format.org"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_text text="humann_Abundance"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">

1:6b7622dda516

            #if $wf.translated_search.protein_db.selector == 'history'
            --protein-database protein_db
            --search-mode '$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.value
            --search-mode 'uniref50'
                #else
            --search-mode 'uniref90'
                #end if
            #end if

                <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
                <option value="mapping">Pre-computed mappings of reads to database sequences</option>
                <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="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"/>
            </when>
            <when value="abundance">

            </when>
        </conditional>
        <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 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>
                <option value="none" selected="true">Run the full workflow steps</option>
            </param>
            <when value="bypass_prescreen">
                <expand macro="nucleotide_search"/>
                <expand macro="translated_search"/>
            </when>
            <when value="bypass_taxonomic_profiling">
                <param argument="--taxonomic-profile" type="data" format="tabular,txt,tsv" label="Taxonomic profile file"/>
                <expand macro="nucleotide_search"/>
                <expand macro="translated_search"/>
            </when>
            <when value="bypass_nucleotide_index">
                <expand macro="nucleotide_search"/>

                <option value="diamond_unaligned">Translated alignment unaligned reads</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
            <filter>out['output_format'] == "biom"</filter>
        </data>
        <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
            <filter>out['output_format'] == "biom"</filter>
        </data>
        <data name="pathabundance_tsv" format="tabular" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
            <filter>out['output_format'] == "tsv"</filter>
        </data>
        <data name="pathabundance_biom" format="biom1" from_work_dir="output/*_pathabundance.biom" label="${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 ${on_string}: Log"/>
        <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/*_temp/*_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" >
            <filter>out['intermediate_temp'] and "metaphlan_bowtie2" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" >
            <filter>out['intermediate_temp'] and "metaphlan_bugs_list" in out['intermediate_temp']</filter>
        </data>
        <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" >
            <filter>out['intermediate_temp'] and "bowtie2_alignment" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >
            <filter>out['intermediate_temp'] and "bowtie2_reduced_alignment" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >
            <filter>out['intermediate_temp'] and "bowtie2_unaligned" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >
            <filter>out['intermediate_temp'] and "custom_chocophlan_database" in out['intermediate_temp']</filter>
        </data>
        <data format="tabular" name="diamond_aligned" from_work_dir="output/*_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >
            <filter>out['intermediate_temp'] and "diamond_aligned" in out['intermediate_temp']</filter>
        </data>
        <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
            <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="12">
            <conditional name="in">

                <param name="remove_statified_output" value="false"/>
                <param name="intermediate_temp" value=""/>
            </section>
            <output name="gene_families_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="biom-format"/>
                    <has_text text="UniRef90_A0A396BPQ7|g__Bacteroides.s__Bacteroides_vulgatus"/>
                    <has_text text="UniRef90_W8YTG4|unclassified"/>
                </assert_contents>
            </output>
            <output name="pathcoverage_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="TREE"/>
                    <has_text text="format-url"/>
                    <has_text text="biom-format"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_text text="humann_Coverage"/>
                </assert_contents>
            </output>
            <output name="pathabundance_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="TREE"/>
                    <has_text text="format-url"/>
                    <has_text text="biom-format"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_text text="humann_Abundance"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">