Mercurial > repos > galaxyp > feature_alignment

comparison feature_alignment.xml @ 2:8559c361b8a1 draft

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author galaxyp
date Mon, 11 May 2015 14:25:57 -0400
parents 25f43048bff3
children 38b0cb816891
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1:25f43048bff3 2:8559c361b8a1
40 40
41 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" /> 41 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" />
42 <param name="max_fdr_quality" type="text" default="-1.0" 42 <param name="max_fdr_quality" type="text" default="-1.0"
43 label="Extension score cutoff" 43 label="Extension score cutoff"
44 help="During the extension phase of the algorithm, peakgroups of this quality will still be considered for alignment (in FDR) - it is possible to give a range in the format lower,higher+stepsize,stepsize - e.g. 0,0.31,0.01 (-1 will set it to fdr_cutoff) (--max_fdr_quality)"/> 44 help="During the extension phase of the algorithm, peakgroups of this quality will still be considered for alignment (in FDR) - it is possible to give a range in the format lower,higher+stepsize,stepsize - e.g. 0,0.31,0.01 (-1 will set it to fdr_cutoff) (--max_fdr_quality)"/>
45 <param name="max_rt_diff" type="integer" default="30" 45 <param name="max_rt_diff" type="integer" value="30" default="30"
46 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/> 46 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/>
47 <param name="iso_max_rt_diff" type="text" default="10" 47 <param name="iso_max_rt_diff" type="text" value="10" default="10"
48 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" /> 48 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" />
49 <param name="frac_selected" type="float" value="0.0" min="0" max="1" 49 <param name="frac_selected" type="float" value="0.0" min="0" max="1"
50 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/> 50 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/>
51 <param name="method" type="select" 51 <param name="method" type="select"
52 label="Which method to use for the clustering" 52 label="Which method to use for the clustering"