comparison cat_bins.xml @ 2:31853794ace2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e

1:18676df0cb3a

<tool id="cat_bins" name="CAT bins" version="@VERSION@.1">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    #set $bin_dir = None
    #if len($mags) > 1:
        #set $bin_dir = 'inputs'
        mkdir -p $bin_dir &&
        #for mag in $mags:
            ln -s '$mag' $bin_dir/ &&
        #end for
    #end if
    CAT 
    #if $bin_dir
        bins -s '.dat' -b '$bin_dir'
    #else
        bin -b '$mags'
    #end if 
    @CAT_DB@
    @USE_INTERMEDIATES@
    @CUSTOM_SETTINGS@
    @DIAMOND_OPTIONS@

        </test>
        <test>
            <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="bin2classification"/>
           <param name="select_outputs" value="predicted_proteins_faa"/>
            <conditional name="names">
                <param name="add_names" value="both"/>
            </conditional>
            <param name="summarise" value="classification"/>
            <output name="predicted_proteins_faa">

                    <has_text text="contig_4403" />
                </assert_contents>
            </output>
            <output name="orf2lca_names">
                <assert_contents>
                    <has_text text="Listeria" />
                    <has_text text="Vibrio" />
                </assert_contents>
            </output>
            <output name="classification_summary">
                <assert_contents>
                    <has_text text="Listeria" />
                </assert_contents>
            </output>
        </test>

    </tests>

2:31853794ace2

<tool id="cat_bins" name="CAT bins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    #import re
    #set $bin_dir = None
    #if len($mags) > 1:
        #set $bin_dir = 'inputs'
        mkdir -p $bin_dir &&
        #for mag in $mags:
            #set input_identifier = re.sub('[^\s\w\-]', '_', str($mag.element_identifier))
            ln -s '$mag' '${bin_dir}/${input_identifier}.FASTA' &&
        #end for
    #else
        #set $bin_file = re.sub('[^\s\w\-]', '_', str($mags[0].element_identifier))
        ln -s $mags[0] '$bin_file' &&
    #end if
    CAT 
    #if $bin_dir
        bins -s '.FASTA' -b '$bin_dir'
    #else
        bin -b '$bin_file'
    #end if 
    @CAT_DB@
    @USE_INTERMEDIATES@
    @CUSTOM_SETTINGS@
    @DIAMOND_OPTIONS@

        </test>
        <test>
            <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="bin2classification"/>
            <param name="select_outputs" value="predicted_proteins_faa"/>
            <param name="fraction" value="0.6"/>
            <conditional name="names">
                <param name="add_names" value="both"/>
            </conditional>
            <param name="summarise" value="classification"/>
            <output name="predicted_proteins_faa">

                    <has_text text="contig_4403" />
                </assert_contents>
            </output>
            <output name="orf2lca_names">
                <assert_contents>
                    <has_text text="Vibrionaceae" />
                    <has_text text="Vibrio" />
                </assert_contents>
            </output>
            <output name="classification_summary">
                <assert_contents>
                    <has_text text="Gammaproteobacteria" />
                </assert_contents>
            </output>
        </test>

    </tests>