annotate meme_chip_wrapper.xml @ 5:31fbc8623795 draft

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<tool id="meme_chip_wrapper" name="meme-chip" version="1.0.0">
    <requirements>
        <requirement type="package" version="4.9.0">meme-chip</requirement>
    </requirements>
    <description></description>
    <version_command>echo "MEME version r4.9.0"</version_command>
    <command> meme-chip $input_file -o ${memechip_out.files_path} 
        #for p in str.split($motif_dbs.fields.path,","):
            -db $p
        #end for

        #if str( $options_type.options_type_selector ) == 'advanced':
            #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
                -bfile "${ str( $options_type.bg_type.bfile ) }"
            #end if

            #if str( $options_type.ccut ) != '-1':
                -ccut "${ str( $options_type.ccut ) }"
            #end if

            #if str( $options_type.time ) != '-1':
                -time "${ str( $options_type.time ) }"
            #end if

            -desc "${ str( $options_type.desc ) }"
            
            #if str( $options_type.meme_mod ) != '':
                -meme-mod "${ str($options_type.meme_mod) }"
            #end if

            #if str( $options_type.meme_minw ) != '-1':
                -meme-minw "${ str($options_type.meme_minw) }"
            #end if

            #if str( $options_type.meme_maxw ) != '-1':
                -meme-maxw "${ str($options_type.meme_maxw) }"
            #end if

            #if str( $options_type.meme_nmotifs ) != '-1':
                -meme-nmotifs "${ str($options_type.meme_nmotifs) }"
            #end if

            #if str( $options_type.meme_minsites ) != '-1':
                -meme-minsites "${ str($options_type.meme_minsites) }"
            #end if

            #if str( $options_type.meme_maxsites ) != '-1':
                -meme-maxsites "${ str($options_type.meme_maxsites) }"
            #end if

            #if $options_type.meme_pal:
                -meme-pal "${ str($options_type.meme_pal) }"
            #end if
            
            #if str( $options_type.dreme_e ) != '-1.0':
                -dreme-e "${ str($options_type.dreme_e) }"
            #end if

            #if str( $options_type.dreme_m ) != '-1':
                -dreme-m "${ str($options_type.dreme_m) }"
            #end if

            #if str($options_type.centrimo_score) != '-1.0':
                -centrimo-score "${ str($options_type.centrimo_score) }"
            #end if

            #if str( $options_type.centrimo_maxreg ) != '-1':
                -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }"
            #end if

            #if str( $options_type.centrimo_ethresh ) != '-1.0':
                -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }"
            #end if

            #if $options_type.centrimo_noseq:
                -centrimo-noseq 
            #end if

        #end if
        <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
        2&gt;&amp;1 || echo "Error running MEME."
        <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}-->
        <!--&amp;&amp; zip -r result $html_outfile.files_path-->
        &amp;&amp; cd ${memechip_out.files_path} 
        &amp;&amp; zip -rp memechip_out ./
        &amp;&amp; mv memechip_out.zip ${memechip_out}
    </command>
    <inputs>
        <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
        <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases">
            <options from_data_table="meme_chip_motifs">
                <filter type="sort_by" column="1"/>
                <validator type="no_options" message="No indexes are available for the selected dataset"/>
            </options>
          
        </param>
        <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True">
            <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
        </param>
        <conditional name="options_type">
            <param name="options_type_selector" type="select" label="Options Configuration">
                <option value="basic" selected="true">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="basic">
            <!-- do nothing here -->
            </when>
            <when value="advanced">
                <!--bfile-->
                <conditional name="bg_type">
                    <param name="bg_type_selector" type="select" label="Custom background">
                        <option value="bg_default" selected="True">Default Background</option>
                        <option value="bg_user">Background in your History</option>
                    </param>
                    <when value="bg_default">
                        <!--do nothing here-->
                    </when>
                    <when value="bg_user">
                        <param name="bfile" type="data" label="-bfile: Background File" />
                    </when>
                </conditional>
                <!--ccut-->
                <param name="ccut" type="integer" value="-1" label="-ccut: Max size of a seq before it is cut down; 0: do not cut; -1: Default behaviour" />
                <!--tine-->
                <param name="time" type="integer" value="-1" label="-time: Maximum time (minutes) that this program has to run and create output in; -1: no limit" />
                <!--desc-->
                <param name="desc" type="text" value="Galaxy MEME-Chip" label="-desc: Description of the analysis" >
                    <sanitizer>
                      <valid initial="string.printable">
                        <remove value="&apos;"/>
                      </valid>
                      <mapping initial="none">
                        <add source="&apos;" target=""/>
                      </mapping>
                    </sanitizer>
                </param>
                <!--MEME options-->
                <param name="meme_mod" type="select" label="-meme-mod: Sites used in a single sequence" >
                    <option value="" selected="True"/>
                    <option value="oops" />
                    <option value="zoops" />
                    <option value="anr" />
                </param>
                <param name="meme_minw" type="integer" value="-1" label="-meme-minw: minimum motif width; -1: Default behaviour" />
                <param name="meme_maxw" type="integer" value="-1" label="-meme-maxw: maximum motif width; -1: Default behaviour" />
                <param name="meme_nmotifs" type="integer" value="-1" label="-meme-nmotifs: maximum number of motifs to find; -1: Default behaviour" />
                <param name="meme_minsites" type="integer" value="-1" label="-meme-minsites: minimum number of sites per motif; -1: Default behaviour" />
                <param name="meme_maxsites" type="integer" value="-1" label="-meme-maxsites: maximum number of sites per motif; -1: Default behaviour" />
                <param name="meme_pal" type="boolean" label="-meme-pal: look for palindromes only" />
                <!--DREME options-->
                <param name="dreme_e" type="float" value="-1" label="-dreme-e: stop searching after reaching this E-value threshold; -1: Default behaviour" />
                <param name="dreme_m" type="integer" value="-1" label="-dreme-e: stop searching after finding this many motifs; -1: Default behaviour" />
                <!--CentriMo options-->
                <param name="centrimo_score" type="float" value="-1" label="-centrimo-score: set the minimum allowed match score; -1: Default behaviour" />
                <param name="centrimo_maxreg" type="integer" value="-1" label="-centrimo-maxreg: set the maximum region size to be considered; -1: Default behaviour" />
                <param name="centrimo_ethresh" type="float" value="-1" label="-centrimo-ethresh: set the E-value threshold for reporting; -1: Default behaviour" />
                <param name="centrimo_noseq" type="boolean" label="-centrimo-noseq: don't store sequence IDs in the output" />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="zip" name="memechip_out" label="${tool.name} on ${on_string} SAVE ME" />
    </outputs>


    <tests>
        <test>
            <param name="input_file" value="extract_genomic_dna.fa" />
            <output name="html_file" file="sample_output.html" ftype="html" />
        </test>
    </tests>

    <help>

        .. class:: infomark

        After the job finishes, save the zip file, unzip and open "index.html"

        The actual meme-chip command is displayed under "Command line summary"

        Defaults:
        http://meme.nbcr.net/meme/doc/meme-chip.html

    </help>
</tool>