comparison macros.xml @ 10:a6fba3d92531 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"

9:ec9cbd6b9a49

    whenever you make changes to the following two version tokens!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually adjust the +galaxy
    version number. -->
    <!-- STAR version to be used -->
    <token name="@VERSION@">2.7.7a</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:
    STAR -h | grep versionGenome

        @FASTQ_GZ_OPTION@
    #end if
    ]]></token>
    <xml name="ref_selection">
        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
        <!-- Currently, this parameter is not exposed in the wrapper,
             but used only in the tests to avoid excessive index sizes for
             the tiny test genomes. -->
        <param name="genomeSAindexNbases" type="hidden" value="" />
    </xml>
    <xml name="stdio" >
        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>
            <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>

                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
            </when>
        </conditional>
    </xml>
    <xml name="umidedup_options">
        <option value="1MM_All" selected="true">All</option>
        <option value="1MM_Directional" >Directional</option>
    </xml>
    <xml name="anchor_types">
        <option value="0">Read start</option>
        <option value="1">Read end</option>
        <option value="2">Adapter start</option>

        <option value="1MM" >Single match</option>
    </xml>
    <xml name="cb_match_wl_cellranger">
        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
    </xml>
</macros>

10:a6fba3d92531

    whenever you make changes to the following two version tokens!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually adjust the +galaxy
    version number. -->
    <!-- STAR version to be used -->
    <token name="@VERSION@">2.7.8a</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:
    STAR -h | grep versionGenome

        @FASTQ_GZ_OPTION@
    #end if
    ]]></token>
    <xml name="ref_selection">
        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
          <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
    </xml>
    <xml name="stdio" >
        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>
            <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>

                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
            </when>
        </conditional>
    </xml>
    <xml name="umidedup_options">
        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
        <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
        <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
    </xml>
    <xml name="anchor_types">
        <option value="0">Read start</option>
        <option value="1">Read end</option>
        <option value="2">Adapter start</option>

        <option value="1MM" >Single match</option>
    </xml>
    <xml name="cb_match_wl_cellranger">
        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
    </xml>
    <xml name="solo_adapter_params">
        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
            <sanitizer>
                <valid initial="string.digits">
                    <add value="-"/>
                    <add value="A"/>
                    <add value="T"/>
                    <add value="C"/>
                    <add value="G"/>
                    <add value="N"/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
        <param argument="--clipAdapterType" type="select" >
            <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
            <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
            <option value="None" >No adapter clipping</option>
        </param>
    </xml>
</macros>