comparison htseq-count.xml @ 8:65c91537862c

Updated to HTSeq 0.5.4p5, use tool shed repository dependencies

7:1615d0b5b809

<tool id="htseq_count" name="htseq-count" version="0.3.1">
    <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
    <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
    <requirements>
        <requirement type="package" version="1.6.2">numpy</requirement>
        <requirement type="package" version="0.5.4p1">htseq</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement> 
    </requirements>
    <command>
    ##set up input files
    #set $reference_fasta_filename = "localref.fa"

The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*.

The following figure illustrates the effect of these three modes:

.. image:: ./static/images/count_modes.png
    :width: 500


Strandedness
------------

8:65c91537862c

<tool id="htseq_count" name="htseq-count" version="0.3.2">
    <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
    <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
    <requirements>
        <requirement type="package" version="1.7.1">numpy</requirement>
        <requirement type="package" version="0.5.4p5">htseq</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement> 
    </requirements>
    <command>
    ##set up input files
    #set $reference_fasta_filename = "localref.fa"

The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*.

The following figure illustrates the effect of these three modes:

.. image:: $PATH_TO_IMAGES/count_modes.png
    :width: 500


Strandedness
------------