comparison kofamscan.xml @ 1:23494763e39e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"

0:24adf43898ec

<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>gene function annotation based on KEGG orthology and HMM</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="reportannotation" token_selected="">
            <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
        </xml>
    </macros>
    <requirements>

        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## preprocessing
mkdir 'profile' &&
#if $p_cond.p_sel == 'compressed'
    tar -xf '${p_cond.p}' -C 'profile' &&
#elif $p_cond.p_sel == 'hmm'
    ## input files require prefix 'K' and file extension '.hmm'
    #for $i, $current in enumerate($p_cond.p)
        ln -s '$current' 'profile/K${i}.hmm' &&
    #end for

                    <has_n_lines n="7"/>
                    <has_line line="sp|P19858|LDHA_BOVIN"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

1:23494763e39e

<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>gene function annotation based on KEGG orthology and HMM</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="reportannotation" token_selected="">
            <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
        </xml>
    </macros>
    <requirements>

        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## preprocessing
mkdir ./profile &&
mkdir ./temp_extract &&
#if $p_cond.p_sel == 'compressed'
    tar -xf '${p_cond.p}' -C temp_extract &&
    find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; &&
    find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; &&
#elif $p_cond.p_sel == 'hmm'
    ## input files require prefix 'K' and file extension '.hmm'
    #for $i, $current in enumerate($p_cond.p)
        ln -s '$current' 'profile/K${i}.hmm' &&
    #end for

                    <has_n_lines n="7"/>
                    <has_line line="sp|P19858|LDHA_BOVIN"/>
                </assert_contents>
            </output>
        </test>
        <!-- #5 -->
        <test expect_num_outputs="1">
            <param name="query" value="query.fasta"/>
            <conditional name="p_cond">
                <param name="p_sel" value="compressed"/>
                <param name="p" value="profilesTyp2.tar.gz"/>
            </conditional>
            <param name="k" value="ko"/>
            <output name="out_result">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**