comparison macros.xml @ 7:62c9df8382c2 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"

6:64be1ac21109

<macros>
    <token name="@VERSION@">0.9.21</token>

    <xml name="requirements">
        <requirements>
          <requirement type="package" version="@VERSION@">diamond</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <!-- disabled error detection by exit code to be able to detect oom errors by 
                 regex, can be reenabled when https://github.com/galaxyproject/galaxy/pull/6338 is merged
            <exit_code range=":-1" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
            <exit_code range="1:" level="fatal"  description="Error occurred. Please check Tool Standard Error" />-->
            <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" />
            <regex match=".+" source="stderr" level="fatal" description=""/>
        </stdio>
    </xml>

    <xml name="version_command">
        <version_command>diamond version</version_command>

                    <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
                    <option value="stitle">Subject Title</option>
                    <option value="salltitles">All Subject Title(s)</option>
                    <option value="qcovhsp">Query Coverage Per HSP</option>
                    <option value="qtitle">Query title</option>
                </param>
            </when>
            <when value="100">
                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>

7:62c9df8382c2

<macros>
    <token name="@VERSION@">0.9.29</token>

    <xml name="requirements">
        <requirements>
          <requirement type="package" version="@VERSION@">diamond</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range=":-1" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
            <exit_code range="1:" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
            <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" />
        </stdio>
    </xml>

    <xml name="version_command">
        <version_command>diamond version</version_command>

                    <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
                    <option value="stitle">Subject Title</option>
                    <option value="salltitles">All Subject Title(s)</option>
                    <option value="qcovhsp">Query Coverage Per HSP</option>
                    <option value="qtitle">Query title</option>
                    <option value="full_qseq">Query sequence</option>
                    <option value="full_sseq">Subject sequence</option>
                    <option value="qqual">Query quality values for the aligned part of the query</option>
                    <option value="full_qqual">Query quality values</option>
                    <option value="qstrand">Query strand</option>
                </param>
            </when>
            <when value="100">
                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>