comparison seqtk_seq.xml @ 9:4b494533146a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6

8:3da72230c066

<?xml version="1.0"?>
<tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@.3">
    <description>common transformation of FASTA/Q</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk seq -q $q
-X $X

        <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
        <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
        <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" />
    </outputs>
    <tests>
        <!-- This is a sorry excuse for a test for a tool which does way more
             than it should, but upstream decided to put a TON of functionality
             into a single tool rather than using the single responsibility

9:4b494533146a

<?xml version="1.0"?>
<tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>common transformation of FASTA/Q</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk seq -q $q
-X $X

        <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
        <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
        <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- This is a sorry excuse for a test for a tool which does way more
             than it should, but upstream decided to put a TON of functionality
             into a single tool rather than using the single responsibility