comparison seqtk_cutN.xml @ 22:f2a792351212 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66

21:ac22e16bfecd

<?xml version="1.0"?>
<tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
    <description>cut sequence at long N</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk cutN
-n $n

        <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
        <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
        <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_cutn.fa"/>
            <param name="n" value="1"/>

22:f2a792351212

<tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>cut sequence at long N</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk cutN
-n $n

        <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
        <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
        <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
    </inputs>
    <outputs>
       <data name="default" format_source="in_file" label="${tool.name} on ${on_string}: split on N runs longer than $n">
            <change_format>
                <when input="g" value="-g" format="bed" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_cutn.fa"/>
            <param name="n" value="1"/>