Mercurial > repos > iuc > transit_gumbel

comparison transit_gumbel.xml @ 3:ecce0cbe659f draft

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"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
comparison
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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