comparison count-median.xml @ 10:570505540a7b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997

9:b3d513c7093e

<tool id="khmer_count_median" name="khmer: Count Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Count the median/avg k-mer abundance for each sequence</description>
    <expand macro="bio_tools"/>
    <macros>
        <token name="@BINARY@">count-median.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -u &&

    <inputs>
        <expand macro="input_sequence_filename" />
        <expand macro="input_countgraph_filename" />
    </inputs>
    <outputs>
        <data name="output_summary_filename" format="txt"
            label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_sequence_filename" value="test-abund-read-2.fa" />

    </tests>
    <help><![CDATA[
Count the median/avg k-mer abundance for each sequence in the input file,
based on the k-mer counts in the given k-mer countgraph. Can be used to
estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The
output file contains sequence id, median, average, stddev, and seq length;
fields are separated by spaces. For khmer 1.x count-median.py will split
sequence names at the first space which means that some sequence formats (e.g.
paired FASTQ in Casava 1.8 format) will yield uninformative names. Use
`--csv` to fix this behavior.

@HELP_FOOTER@

10:570505540a7b

<tool id="khmer_count_median" name="khmer: Count Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Count the median/avg k-mer abundance for each sequence</description>
    <macros>
        <token name="@BINARY@">count-median.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -u &&

    <inputs>
        <expand macro="input_sequence_filename" />
        <expand macro="input_countgraph_filename" />
    </inputs>
    <outputs>
        <data name="output_summary_filename" format="csv"
            label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_sequence_filename" value="test-abund-read-2.fa" />

    </tests>
    <help><![CDATA[
Count the median/avg k-mer abundance for each sequence in the input file,
based on the k-mer counts in the given k-mer countgraph. Can be used to
estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The
output file contains sequence id, median, average, stddev, and seq length.
For khmer 1.x count-median.py will split
sequence names at the first space which means that some sequence formats (e.g.
paired FASTQ in Casava 1.8 format) will yield uninformative names. Use
`--csv` to fix this behavior.

@HELP_FOOTER@