Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]
Algorithm options:
-t INT number of threads [1]
-k INT minimum seed length [19]
-w INT band width for banded alignment [100]
-d INT off-diagonal X-dropoff [100]
-r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
-y INT seed occurrence for the 3rd round seeding [20]
-c INT skip seeds with more than INT occurrences [500]
-D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
-W INT discard a chain if seeded bases shorter than INT [0]
-m INT perform at most INT rounds of mate rescues for each read [50]
-S skip mate rescue
-P skip pairing; mate rescue performed unless -S also in use
-e discard full-length exact matches
Scoring options:
-A INT score for a sequence match, which scales options -TdBOELU unless overridden [1]
-B INT penalty for a mismatch [4]
-O INT[,INT] gap open penalties for deletions and insertions [6,6]
-E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]
-L INT[,INT] penalty for 5'- and 3'-end clipping [5,5]
-U INT penalty for an unpaired read pair [17]
-x STR read type. Setting -x changes multiple parameters unless overriden [null]
pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)
ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)
intractg: -B9 -O16 -L5 (intra-species contigs to ref)
Input/output options:
-p smart pairing (ignoring in2.fq)
-R STR read group header line such as '@RG\tID:foo\tSM:bar' [null]
-H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]
-j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)
-v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
-T INT minimum score to output [30]
-h INT[,INT] if there are <INT hits with score >80% of the max score, output all in XA [5,200]
-a output all alignments for SE or unpaired PE
-C append FASTA/FASTQ comment to SAM output
-V output the reference FASTA header in the XR tag
-Y use soft clipping for supplementary alignments
-M mark shorter split hits as secondary
-I FLOAT[,FLOAT[,INT[,INT]]]
specify the mean, standard deviation (10% of the mean if absent), max
(4 sigma from the mean if absent) and min of the insert size distribution.
FR orientation only. [inferred]
Note: Please read the man page for detailed description of the command line and options.
@jmchilton here are a few examples:
ctd/CVInspector.ctd: <ITEMLIST name="ignore_cv" type="string" description="A list of CV identifiers
which should be ignored." required="false" advanced="false">
ctd/CVInspector.ctd: <LISTITEM value="UO"/>
ctd/CVInspector.ctd: <LISTITEM value="PATO"/>
ctd/CVInspector.ctd: <LISTITEM value="BTO"/>
ctd/CVInspector.ctd: </ITEMLIST>
<ITEMLIST name="target_modifications" type="string" description="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'" required="false" advanced="false" restrictions="15N-oxobutanoic (N-term C),2-dimethylsuccinyl (C),2-monomethylsuccinyl (C),2-nitrobenzyl (Y),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3-phosphoglyceryl (K),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),a-type-ion (C-term),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:13C(2) (K),Acetyl:2H(3) (H),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Acetyl:2H(3)...">
<LISTITEM value="Phospho (S)"/>
<LISTITEM value="Phospho (T)"/>
<LISTITEM value="Phospho (Y)"/>
</ITEMLIST>
Since both cases don't have restrictions we can't render them as <select> and repeats don't work, because I can't set the defaults.
My favorite solution would be a select where the user can add values.
<param><value></value></param>
does not work in a test :(
Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse file tool_data_table_conf.xml.sample: Merging tabular data tables with non matching columns is not allowed: twobit:{'path': 1, 'name': 0, 'value': 0} != twobit:{'value': 1, 'dbkey': 0, 'name': 1}"}
should_not_be_noarch_source
when there is no noarch
makes no sense
planemo serve
, it's still using the older version. What change must I make to have it use the newer bioconda-recipes version? (Note, if I do conda install toolname
on the command line, it installs the new version.)
2.006
instead of 2.0013
. I think I probably need to bump the wrapper version. I was using some weird version spec and I see that the latest spec says that the <tool version attribute should be tool_version+wrapper_version. I only had wrapper_version.
planemo serve
from the main tool repo directory instead of the specific tool directory and it happened to use the new version when I ran it. Now if I run it from either, it uses the new version. I don't understand it. https://github.com/hepcat72/robs_galaxy_tools/tree/vcfsc13/tools/vcfsamplecompare