comparison cmscan.xml @ 8:c9e29ac5d099 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"

7:477d829d3250

<tool id="infernal_cmscan" name="cmscan" version="@VERSION@.0">
    <description> Search sequences against collections of covariance models</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command>
<![CDATA[
    ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
    ## it will be converted to a tab delimited file and piped to Galaxy
    temp_tabular_output=\$(mktemp) &&

            ##'$cm_opts.cmfile'
            cmdb.cm
        #end if
        ## sequence file
        '$seqdb'
        &&
        sed 's/ \+ /\t/g' '\$temp_tabular_output' > '$outfile'

]]>
    </command>
    <inputs>
        <param name="seqdb" type="data" format="fasta" label="Sequence database &lt;seqfile&gt;"/>

                label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
            <param argument="--toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean"
                label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>

        </section>



    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="cmscan on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <conditional name="cm_opts">
                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="minifam.cm" />
            </conditional>
            <param name="aux_files" value="minifam.tar" ftype="tar"/>
            <param name="seqdb" value="metag-example.fa"/>
            <output name="outfile">
                <assert_contents>
                    <has_text text="AAGA01015927.1"/>
                </assert_contents>
            </output>
        </test>

8:c9e29ac5d099

<tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description> Search sequences against collections of covariance models</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="xrefs"/>
    <command>
<![CDATA[
    ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
    ## it will be converted to a tab delimited file and piped to Galaxy
    temp_tabular_output=\$(mktemp) &&

            ##'$cm_opts.cmfile'
            cmdb.cm
        #end if
        ## sequence file
        '$seqdb'
        ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984
        ## remove the header
        && tail -n +3 '\$temp_tabular_output' > headless_file
        ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk)
        && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column
        ## fix the tabulation the rest content (except the description column)
        && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file
        ## add the description column to the tabulated data
        && paste -d"\t" tabulated_columns description_column > joined_file
        ## include a correct header
        && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header
        ## export the result
        && cat header joined_file > '$outfile'

]]>
    </command>
    <inputs>
        <param name="seqdb" type="data" format="fasta" label="Sequence database &lt;seqfile&gt;"/>

                label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
            <param argument="--toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean"
                label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>

        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="cmscan on ${on_string}"/>

    </outputs>
    <tests>
        <test>
            <conditional name="cm_opts">
                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="minifam.cm" />
            </conditional>
            <param name="aux_files" value="minifam.tar" ftype="tar"/>
            <param name="seqdb" value="metag-example.fa"/>
            <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8">
                <assert_contents>
                    <has_n_lines n="15"/>
                    <has_text text="AAGA01015927.1"/>
                </assert_contents>
            </output>
        </test>