comparison count-median.xml @ 7:77410799e8e9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"

6:7aa811aa3b93

<tool id="khmer_count_median" name="Count Median" version="@WRAPPER_VERSION@.0">
    <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="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -xu &&
@BINARY@
$input_countgraph_filename
$input_sequence_filename
$output_summary_filename
]]>

        <expand macro="input_sequence_filename" />
        <expand macro="input_countgraph_filename" />
    </inputs>
    <outputs>
        <data name="output_summary_filename" format="txt"
            label="${input_sequence_filename} sequence id, median, average, stddev, and seq length" />
    </outputs>
    <tests>
        <test>
            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />

7:77410799e8e9

<tool id="khmer_count_median" name="khmer: Count Median" version="@WRAPPER_VERSION@@TOOL_VERSION@">
    <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="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -u &&
@BINARY@
$input_countgraph_filename
$input_sequence_filename
$output_summary_filename
]]>

        <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" />
            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />