Mercurial > repos > iuc > transit_gumbel
comparison transit_gumbel.xml @ 3:ecce0cbe659f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
| author | iuc |
|---|---|
| date | Wed, 16 Oct 2019 04:32:08 -0400 |
| parents | c980be2c002c |
| children | f50807720df1 |
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| 2:c980be2c002c | 3:ecce0cbe659f |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="transit_gumbel" name="Gumbel" version="@VERSION@+galaxy1"> | 2 <tool id="transit_gumbel" name="Gumbel" version="@VERSION@+galaxy2"> |
| 3 <description>- determine essential genes</description> | 3 <description>- determine essential genes</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 12 -s $samples -b $burnin -m $smallest -t $trim | 12 -s $samples -b $burnin -m $smallest -t $trim |
| 13 ]]> | 13 ]]> |
| 14 </command> | 14 </command> |
| 15 <inputs> | 15 <inputs> |
| 16 <expand macro="standard_inputs"> | 16 <expand macro="standard_inputs"> |
| 17 <expand macro="handle_replicates" /> | |
| 17 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" /> | 18 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" /> |
| 18 <param name="burnin" argument="-b" type="integer" value="500" label="Number of Burn-in samples" /> | 19 <param name="burnin" argument="-b" type="integer" value="500" label="Number of Burn-in samples" /> |
| 19 <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" /> | 20 <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" /> |
| 20 <param name="trim" argument="-t" type="integer" value="1" label="Trimming interval for values" /> | 21 <param name="trim" argument="-t" type="integer" value="1" label="Trimming interval for values" /> |
| 21 </expand> | 22 </expand> |
| 66 Optional Arguments: | 67 Optional Arguments: |
| 67 -s <integer> := Number of samples. Default: -s 10000 | 68 -s <integer> := Number of samples. Default: -s 10000 |
| 68 -b <integer> := Number of Burn-in samples. Default -b 500 | 69 -b <integer> := Number of Burn-in samples. Default -b 500 |
| 69 -m <integer> := Smallest read-count to consider. Default: -m 1 | 70 -m <integer> := Smallest read-count to consider. Default: -m 1 |
| 70 -t <integer> := Trims all but every t-th value. Default: -t 1 | 71 -t <integer> := Trims all but every t-th value. Default: -t 1 |
| 71 -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum | 72 -r <string> := How to handle replicates. Sum or Mean. Default: -r Mean |
| 72 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 | 73 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 |
| 73 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 | 74 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 |
| 74 -n <string> := Determines which normalization method to use. Default -n TTR | 75 -n <string> := Determines which normalization method to use. Default -n TTR |
| 75 | 76 |
| 76 | 77 |