Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 8:4e7f59d5ee18 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit e27d18d58ae095e7fad4b08b04370857a1d37964-dirty
author drosofff
date Tue, 02 Feb 2016 11:50:13 -0500
parents 9784e5046f04
children 44a0b0fa52a9
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7:9784e5046f04 8:4e7f59d5ee18
75 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> 75 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> 76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> 77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> 78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> 79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
80 <param name="yrange" type="integer" size="6" value="0" label="y axis range" help="leave at 0 for autoscaling"/>
80 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> 81 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
81 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> 82 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
82 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> 83 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
83 </param> 84 </param>
84 </inputs> 85 </inputs>
125 126
126 plot_size_distribution= function(df, ...) { 127 plot_size_distribution= function(df, ...) {
127 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} 128 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
128 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0, 129 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
129 horizontal=FALSE, 130 horizontal=FALSE,
130 group=polarity, 131 group=polarity,
131 stack=TRUE, 132 stack=TRUE,
132 col=c('red', 'blue'), 133 col=c('red', 'blue'),
133 cex=0.75, 134 cex=0.75,
134 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ), 135 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
135 prepanel=smR.prepanel, 136 prepanel=smR.prepanel,
136 xlab = NULL, 137 xlab = NULL,