comparison bwa_wrapper.xml @ 1:2ba834228e9b draft

Uploaded

0:8d92246f41bb

          --rgpi="${params.readGroup.rgpi}"
          --rgpl="${params.readGroup.rgpl}"
          --rgpu="${params.readGroup.rgpu}"
          --rgsm="${params.readGroup.rgsm}"
        #end if
	#if $params.readGroup.specReadGroup == "from_file"
          --meta_tsv="$params.readGroup.metadata_tsv"
        #end if
      #end if

      ## suppress output SAM header

        <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" />
        <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" />
        <conditional name="readGroup">
          <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
            <option value="yes">Yes</option>
            <option value="no" selected="True">No</option>
          </param>
          <when value="yes">
            <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG 
tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group 

1:2ba834228e9b

          --rgpi="${params.readGroup.rgpi}"
          --rgpl="${params.readGroup.rgpl}"
          --rgpu="${params.readGroup.rgpu}"
          --rgsm="${params.readGroup.rgsm}"
        #end if
        #if $params.readGroup.specReadGroup == "from_file"
          --meta_tsv="$params.readGroup.metadata_tsv"
        #end if
      #end if

      ## suppress output SAM header

        <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" />
        <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" />
        <conditional name="readGroup">
          <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
            <option value="yes">Yes</option>
            <option value="from_file">From File</option>
            <option value="no" selected="True">No</option>
          </param>
          <when value="yes">
            <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG 
tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group