comparison macros.xml @ 1:b955346ef41e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"

0:18b91d72794b

                    </action>
                </when>
            </conditional>
        </actions>
    </macro>
    <macro name="reference_source_cond">
        <conditional name="ref_source_cond">
            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
                <option value="cached" selected="True">Use a cached reference</option>
                <option value="history">Use a reference from the history</option>

                        <validator type="no_options" message="A built-in reference genome is not available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="Using reference genome">
                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
                </param>
            </when>
        </conditional>
    </macro>
    <xml name="citations">
        <citations>
            <citation type="doi">

1:b955346ef41e

                    </action>
                </when>
            </conditional>
        </actions>
    </macro>
    <macro name="input_type_cond">
        <conditional name="input_type_cond">
            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
                <option value="single" selected="true">Single dataset</option>
                <option value="pair">Dataset pair</option>
                <option value="paired">List of dataset pairs</option>
            </param>
            <when value="single">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
            </when>
            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
            </when>
        </conditional>
    </macro>
    <macro name="reference_source_cond">
        <conditional name="ref_source_cond">
            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
                <option value="cached" selected="True">Use a cached reference</option>
                <option value="history">Use a reference from the history</option>

                        <validator type="no_options" message="A built-in reference genome is not available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="Using reference genome"/>
            </when>
        </conditional>
    </macro>
    <macro name="ktrim_cond">
        <conditional name="ktrim_cond">
            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="ktrim"  type="select" label="Select trimming position">
                    <option value="r">Trim to the right</option>
                    <option value="l">Trim to the left</option>
                </param>
                <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
             </when>
        </conditional>
    </macro>
    <xml name="citations">
        <citations>
            <citation type="doi">