Mercurial > repos > evan > bwa_wrappers
comparison bwa_wrapper.xml @ 1:2ba834228e9b draft
Uploaded
| author | evan |
|---|---|
| date | Fri, 06 Jun 2014 12:39:56 -0400 |
| parents | 8d92246f41bb |
| children |
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| 0:8d92246f41bb | 1:2ba834228e9b |
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| 66 --rgpi="${params.readGroup.rgpi}" | 66 --rgpi="${params.readGroup.rgpi}" |
| 67 --rgpl="${params.readGroup.rgpl}" | 67 --rgpl="${params.readGroup.rgpl}" |
| 68 --rgpu="${params.readGroup.rgpu}" | 68 --rgpu="${params.readGroup.rgpu}" |
| 69 --rgsm="${params.readGroup.rgsm}" | 69 --rgsm="${params.readGroup.rgsm}" |
| 70 #end if | 70 #end if |
| 71 #if $params.readGroup.specReadGroup == "from_file" | 71 #if $params.readGroup.specReadGroup == "from_file" |
| 72 --meta_tsv="$params.readGroup.metadata_tsv" | 72 --meta_tsv="$params.readGroup.metadata_tsv" |
| 73 #end if | 73 #end if |
| 74 #end if | 74 #end if |
| 75 | 75 |
| 76 ## suppress output SAM header | 76 ## suppress output SAM header |
| 132 <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" /> | 132 <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" /> |
| 133 <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" /> | 133 <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" /> |
| 134 <conditional name="readGroup"> | 134 <conditional name="readGroup"> |
| 135 <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> | 135 <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> |
| 136 <option value="yes">Yes</option> | 136 <option value="yes">Yes</option> |
| 137 <option value="from_file">From File</option> | |
| 137 <option value="no" selected="True">No</option> | 138 <option value="no" selected="True">No</option> |
| 138 </param> | 139 </param> |
| 139 <when value="yes"> | 140 <when value="yes"> |
| 140 <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 | 141 <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 |
| 141 tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group | 142 tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group |