comparison galaxy-conf/RollingReadLength.xml @ 12:81d5b81fb3c2 draft

Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.

11:b1952a90d4bf

<tool id="RollingReadLength" name="Compute read length" version="1.0.0">
  <description>from paired-end sequencing reads</description>
  <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
  <inputs>
      <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
  </inputs>
  <outputs>
      <data format="wig" name="output" />
  </outputs>
  
<help>
.. class:: warningmark

This tool requires paired-end SAM, BAM, or Bed formatted data. Using single-end data will result in a constant read length.
</help>
</tool>

12:81d5b81fb3c2

<tool id="RollingReadLength" name="Compute mean fragment length" version="1.0.0">
  <description>over each locus</description>
  <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
  <inputs>
      <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
  </inputs>
  <outputs>
      <data format="wig" name="output" />
  </outputs>
  
<help>
  
This tool will compute the mean length of all fragments overlapping a given locus, and can be used to identify sites with exceptionally long or short reads.
  
.. class:: warningmark

This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.

</help>
</tool>