comparison macros.xml @ 6:cab19c0452c4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

5:1af48f9cc27b

<macros>
    <token name="@TOOL_VERSION@">39.06</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
            <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
        </edam_operations>
    </xml>
    <xml name="bio.tools">
        <xrefs>
            <xref type="bio.tools">bbtools</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
            <requirement type="package" version="1.19.2">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
        </requirements>
    </xml>
    <macro name="dbKeyActionsBBMap">
        <expand macro="dbKeyActions">
            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">

            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads 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">

            </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">
                https://doi.org/10.1371/journal.pone.0185056
            </citation>
        </citations>
    </xml>
</macros>

6:cab19c0452c4

<macros>
    <token name="@TOOL_VERSION@">39.08</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic>
            <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic>
            <!-- Bioinformatics -->
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0496</edam_operation>
            <!-- Global alignment -->
            <edam_operation>operation_0491</edam_operation>
            <!-- Pairwise sequence alignment -->
        </edam_operations>
    </xml>
    <xml name="bio.tools">
        <xrefs>
            <xref type="bio.tools">bbtools</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
            <requirement type="package" version="1.20">samtools</requirement>
            <!-- automatic solving installs 1.6 in some cases, instead -->
        </requirements>
    </xml>
    <macro name="dbKeyActionsBBMap">
        <expand macro="dbKeyActions">
            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">

            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Collection of fastqsanger paired read files" collection_type="paired"/>
            </when>
        </conditional>
    </macro>
    <macro name="reference_source_cond">
        <conditional name="ref_source_cond">

            </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">
                https://doi.org/10.1371/journal.pone.0185056
            </citation>
        </citations>
    </xml>
</macros>