# HG changeset patch
# User drosofff
# Date 1454431813 18000
# Node ID 4e7f59d5ee18a293fbe285a57cebcc99d02414ac
# Parent  9784e5046f042deaa139b8f9c292f17a877bf923
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit e27d18d58ae095e7fad4b08b04370857a1d37964-dirty

diff -r 9784e5046f04 -r 4e7f59d5ee18 readmap.xml
--- a/readmap.xml	Thu Nov 26 11:55:39 2015 -0500
+++ b/readmap.xml	Tue Feb 02 11:50:13 2016 -0500
@@ -77,6 +77,7 @@
                 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
                 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
                 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
+                <param name="yrange" type="integer" size="6" value="0" label="y axis range" help="leave at 0 for autoscaling"/>
                 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
                 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
 		  <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
@@ -127,8 +128,8 @@
           smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
           bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
             horizontal=FALSE,
-	    group=polarity,
-	    stack=TRUE,
+            group=polarity,
+            stack=TRUE,
             col=c('red', 'blue'),
             cex=0.75,
             scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
diff -r 9784e5046f04 -r 4e7f59d5ee18 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 26 11:55:39 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 02 11:50:13 2016 -0500
@@ -7,10 +7,10 @@
       <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="f9289486f06d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="fc6f5ca8aef3" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
         <repository changeset_revision="d243626801e2" name="package_biocbasics_2_14" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />