comparison cmsearch.xml @ 19:94cc7ef25867 draft

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

18:3800a5fbb327

<tool id="infernal_cmsearch" name="cmsearch" version="@VERSION@.0">
    <description>Search covariance model(s) against a sequence database </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism>
    <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) &&

            $cyk
            $acyk
            $notrunc
            $anytrunc
            $nonull3
            #if $smxsize <> 128.0
                --smxsize $smxsize
            #end if
            #if $mxsize <> 128.0
                --mxsize $mxsize
            #end if
            --tblout \$temp_tabular_output
            $g
            #if $Z

                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="cmsearch_input1.cm"/>
            </conditional>
            <param name="seqdb" value="cmsearch_input2.fa"/>
            <output name="outfile" file="cmsearch_result.tabular"/>

        </test>
    </tests>

    <help>
<![CDATA[

19:94cc7ef25867

<tool id="infernal_cmsearch" name="cmsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Search covariance model(s) against a sequence database </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
    <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) &&

            $cyk
            $acyk
            $notrunc
            $anytrunc
            $nonull3
            #if str($smxsize) != "128.0"
                --smxsize $smxsize
            #end if
            #if str($mxsize) != "128.0"
                --mxsize $mxsize
            #end if
            --tblout \$temp_tabular_output
            $g
            #if $Z

                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="cmsearch_input1.cm"/>
            </conditional>
            <param name="seqdb" value="cmsearch_input2.fa"/>
            <output name="outfile" file="cmsearch_result.tabular"/>
        </test>
    </tests>

    <help>
<![CDATA[