comparison bam_stat.xml @ 1:cd2daa987b69 draft default tip

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827

0:306127635959

    <expand macro="stdio" />

    <version_command><![CDATA[bam_stat.py --version]]></version_command>

    <command><![CDATA[
        bam_stat.py -i $input -q $mapqual 2> $output
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
        <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
    </inputs>

    <outputs>
        <data format="txt" name="output" />
    </outputs>

    <help><![CDATA[
bam_stat.py
+++++++++++

This program is used to calculate reads mapping statistics from provided BAM
file.  This script determines "uniquely mapped reads" from `mapping quality`_,
which quality the probability that a read is misplaced (Do NOT confused with
sequence quality, sequence quality measures the probability that a base-calling
was wrong) .

Inputs

Input BAM/SAM file
	Alignment file in BAM/SAM format.

Minimum mapping quality
	Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30)

Output
++++++++++++++

- Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}

1:cd2daa987b69

    <expand macro="stdio" />

    <version_command><![CDATA[bam_stat.py --version]]></version_command>

    <command><![CDATA[
        bam_stat.py -i $input -q $mapq 2> $output
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
        <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
    </inputs>

    <outputs>
        <data format="txt" name="output" />
    </outputs>

    <help><![CDATA[
bam_stat.py
+++++++++++

This program is used to calculate reads mapping statistics from provided BAM
file.  This script determines "uniquely mapped reads" from `mapping quality
<http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
which quality the probability that a read is misplaced (Do NOT confused with
sequence quality, sequence quality measures the probability that a base-calling
was wrong) .

Inputs

Input BAM/SAM file
	Alignment file in BAM/SAM format.

Minimum mapping quality
	Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)

Output
++++++++++++++

- Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}