comparison combine_metaphlan2_humann2.xml @ 1:e25efca0a49c draft

"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"

0:31394a0c0242

<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
    <description>to relate genus/species abundances and gene families/pathways abundances</description>

    <requirements>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>

    <version_command></version_command>

    <command><![CDATA[
        python $__tool_directory__/combine_metaphlan2_humann2.py 
            --metaphlan2_file $metaphlan2_file
            --humann2_file $humann2_file
            --type $type    

            #if str($type) == 'gene_families'
                --output_file $gene_families_output_file
            #else
                --output_file $pathway_output_file
            #end if
    ]]></command>

    <inputs>
        <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
        
        <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>

        <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
            <option value="gene_families" selected="true">Gene families</option>
            <option value="pathways">Pathways</option>
        </param>
    </inputs>

    <outputs>
        <data name="gene_families_output_file" format="tabular"
            label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
            <filter>type=="gene_families"</filter>
        </data>
        <data name="pathway_output_file" format="tabular"
            label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
            <filter>type=="pathways"</filter>
        </data>
    </outputs>

    <tests>
    	<test>
    		 <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
    		 <param name="humann2_file" value="humann2_gene_families_input.tabular"/>
    		 <param name='type' value="gene_families"/>
    		 <output name="gene_families_output_file" file="gene_families_output.tabular"/>
    	</test>
    	<test>
    		 <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
    		 <param name="humann2_file" value="humann2_pathways_input.tabular"/>
    		 <param name='type' value="pathways"/>
    		 <output name="pathway_output_file" file="pathways_output.tabular"/>
    	</test>
    </tests>

    <help><![CDATA[
**What it does**

This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs.

For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus.
    ]]></help>

    <citations>
    </citations>
</tool>

1:e25efca0a49c

<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.2.0">
    <description>to relate genus/species abundances and gene families/pathways abundances</description>
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command></version_command>
    <command><![CDATA[
        python $__tool_directory__/combine_metaphlan2_humann2.py 
            --metaphlan2_fp '$metaphlan2_file'
            --humann2_fp '$humann2_file'
            --type '$type'   

            #if str($type) == 'gene_families'
                --output_fp '$gene_families_output_file'
            #else
                --output_fp '$pathway_output_file'
            #end if
    ]]></command>
    <inputs>
        <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
        <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
        <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
            <option value="gene_families" selected="true">Gene families</option>
            <option value="pathways">Pathways</option>
        </param>
    </inputs>
    <outputs>
        <data name="gene_families_output_file" format="tabular"
            label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
            <filter>type=="gene_families"</filter>
        </data>
        <data name="pathway_output_file" format="tabular"
            label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
            <filter>type=="pathways"</filter>
        </data>
    </outputs>
    <tests>
    	<test>
    		<param name="metaphlan2_file" value="metaphlan2_input.txt"/>
    		<param name="humann2_file" value="humann2_gene_families_input.tabular"/>
    		<param name='type' value="gene_families"/>
    		<output name="gene_families_output_file">
                <assert_contents>
                    <has_n_columns n="8"/>
                    <has_n_lines n="29434"/>
                    <has_text text="Staphylococcus_epidermidis"/>
                    <has_text text="Putative transposon Tn552 DNA invertase bin3"/>
                    <has_size value="3467947"/>
                </assert_contents>
            </output>
    	</test>
    	<test>
    		 <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
    		 <param name="humann2_file" value="humann2_pathways_input.tabular"/>
    		 <param name='type' value="pathways"/>
             <output name="pathway_output_file">
                <assert_contents>
                    <has_n_columns n="8"/>
                    <has_n_lines n="1533"/>
                    <has_text text="Rhodobacter_sphaeroides"/>
                    <has_text text="superpathway of acetyl CoA biosynthesis"/>
                    <has_size value="186363"/>
                </assert_contents>
            </output>
    	</test>
    </tests>
    <help><![CDATA[
**What it does**

This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs.

For each gene families/pathways and the corresponding taxonomic stratification, 
you get relative abundance of this gene family/pathway and the relative abundance 
of corresponding species and genus.
    ]]></help>
    <citations>
    </citations>
</tool>