comparison bigscape.xml @ 3:3447eb0ce896 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4

2:ad2f19722a0e

<tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.9</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">BiG-SCAPE</xref>
    </xrefs>
    <requirements>

        #set $path_to_html = $html.files_path
        mkdir -p '$path_to_html' result input &&
        #for $files in $inputdir:
            #set $filename = "region." + $files.element_identifier
            ln -s '$files' './input/$filename' &&
        #end for

        mkdir pfam && 
        ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' &&
        hmmpress './pfam/Pfam-A.hmm' &&

                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="5">
            <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
            <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
            <param name="log" value="true" />
            <param name="clans_off" value="true" />
        </test>
    </tests>
    <help> 

3:3447eb0ce896

<tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.9</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">BiG-SCAPE</xref>
    </xrefs>
    <requirements>

        #set $path_to_html = $html.files_path
        mkdir -p '$path_to_html' result input &&
        #for $files in $inputdir:
            #set $filename = "region." + $files.element_identifier
            ln -s '$files' './input/${filename}.gbk' &&
        #end for

        mkdir pfam && 
        ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' &&
        hmmpress './pfam/Pfam-A.hmm' &&

                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="5">
            <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
            <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
            <param name="log" value="true" />
            <param name="clans_off" value="true" />
        </test>
        <test expect_num_outputs="5">
            <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
            <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk" ftype="genbank" />
            <param name="log" value="true" />
            <param name="clans_off" value="true" />
        </test>
    </tests>
    <help>