comparison make.contigs.xml @ 1:3dab7d200c10 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2

0:2b3fac454f43

        @SHELL_OPTIONS@

        ## Symlinks creation or On the fly creation of a combo file
        #if $input_type.type == 'list_collection'
            #for $pair in $input_type.list_paired_collection:
                echo -e "${pair.name}\t${pair.forward}\t${pair.reverse}" >> combo_fastq.dat &&
            #end for
        #elif $input_type.type == 'simple_collection'
            ln -s '$input_type.paired_collection.forward' ffastq.dat &&
            ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
        #else

                                <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
                            </collection>
                        </element>
                        <element name="Pair2">
                            <collection type="paired">
                                <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
                                <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
                            </collection>
                        </element>
                    </collection>
                </param>
            </conditional>
            <output name="fasta" md5="dab69a0e36f718b55d8defad26ec469b" ftype="fasta"/>
            <output name="qual" md5="cdba5409e4f87e3cd093a4e51084d616" ftype="qual"/>
            <output name="report" md5="80b992abd7e4d6a5e89fa70011ef2384" ftype="txt"/>
            <output name="group" md5="2be2adb030c4fc001bfac7e1172b40e1" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

1:3dab7d200c10

        @SHELL_OPTIONS@

        ## Symlinks creation or On the fly creation of a combo file
        #if $input_type.type == 'list_collection'
            #for $pair in $input_type.list_paired_collection:
                ln -s ${pair.forward} `basename ${pair.forward}` &&
                ln -s ${pair.reverse} `basename ${pair.reverse}` &&
                echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
            #end for
        #elif $input_type.type == 'simple_collection'
            ln -s '$input_type.paired_collection.forward' ffastq.dat &&
            ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
        #else

                                <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
                            </collection>
                        </element>
                        <element name="Pair2">
                            <collection type="paired">
                                <element name="forward" value="test_forward.fastq" />
                                <element name="reverse" value="test_reverse.fastq" />
                            </collection>
                        </element>
                    </collection>
                </param>
            </conditional>
            <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
            <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
            <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
            <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[