view macros.xml @ 2:bddb48f621d5 draft default tip

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty

<macros>
    <token name="@TOOL_VERSION@">6.12.3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code level="fatal" range="1:" description="Error"/>
            <regex match="There is insufficient memory for the Java Runtime Environment" source="stdout" level="fatal_oom" description="Out of memory" />
    </stdio>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[./daa2rma |& grep version | sed 's/.*version \([0-9.]\+\),.*/\1/']]></version_command>
</xml>
    <token name="@CLASSIFICATION_UTILS@"><![CDATA[
#def get_mapping($var, $category, $target)
    #if $var.has_key($category+$target):
        #set m=""
        #if $var.has_key($category+$target+"_select") and $var[$category+$target+"_select"]=='indexed':
            #if $var[$category+$target]
               #set m=str($var[$category+$target].fields.path)
            #end if
        #else
            #set m=str($var[$category+$target])
        #end if
        #if $m!="" and $m!=None and m!="None":
            #return "--"+$category+$target+" "+$m
        #end if
    #else
        #return ""
    #end if
#end def

#def get_mapping_history_indexed($var, $category, $target):
    #if $var.has_key( $category+$target+'_cond' ):
        #return $get_mapping($var[$category+$target+'_cond'], $category, $target)
    #else
        #return $get_mapping($var, $category, $target)
    #end if
#end def

#def get_mapping_acc_gi( $section, $category, $target ):
    #if category in ['gi2','acc2'] and $section.has_key('acc_or_gi_cond'):
        #return $get_mapping_history_indexed($section.acc_or_gi_cond, $category, $target)
    #else:
        #return $get_mapping_history_indexed($section, $category, $target)
    #end if
#end def
    ]]></token>
    <xml name="mapping" token_varname="myvar" token_label="mylabel">
        <conditional name="@VARNAME@_cond">
            <param name="@VARNAME@_select" type="select" label="@LABEL@"> 
                <option value="indexed">Use a built-in mapping</option>
                <option value="history">Use a mapping from the history</option>
            </param>
            <when value="indexed">
                <param argument="--@VARNAME@" type="select" optional="true" label="mapping" >
                    <options from_data_table="megan_tools">
                        <filter type="static_value" column="2" value="@VARNAME@" keep="true"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param argument="--@VARNAME@" type="data" format="tabular" optional="true" label="mapping" />
            </when>
        </conditional>
    </xml>
    <xml name="mappings_gi_acc_syn" token_target="mytarget" token_targetlabel="mytargetlabel">
        <section  name="section_@TARGET@" title="@TARGETLABEL@ Mappings" expanded="false">
            <conditional name="acc_or_gi_cond">
                <param name="acc_or_gi_select" type="select" label="Mapping from GI/Accession" help="use GI for NR releases until August 2016, containing GI numbers"> 
                    <option value="acc">Accession</option>
                    <option value="gi">GI</option>
                </param>
                <when value="gi">
                    <expand macro="mapping" varname="gi2@TARGET@" label="GI-to-@TARGETLABEL@ mapping"/>
                </when>
                <when value="acc">
                    <expand macro="mapping" varname="acc2@TARGET@" label="Accession-to-@TARGETLABEL@ mapping"/>
                </when>
            </conditional>
            <expand macro="mapping" varname="syn2@TARGET@" label="Synonyms-to-@TARGETLABEL@ mapping"/>
            <yield/>
        </section>
    </xml>

    <xml name="mappings_gi_acc_syn_tags" token_target="mytarget" token_targetlabel="mytargetlabel">
        <expand macro="mappings_gi_acc_syn" target="@TARGET@" targetlabel="@TARGETLABEL@">
            <param argument="--tags4@TARGET@" type="data" format="tabular" optional="true" label="Tags for @TARGETLABEL@ id parsing" help="(must set to activate id parsing)"/>
        </expand>
    </xml>

    <token name="@MDF_CLI@"><![CDATA[
#if $metaDataFile:
    -mdf
    #for $m in $metaDataFile
        #if $m
            '$m'
        #end if
    #end for
#end if
    ]]></token>
    <xml name="mdf_macro">
        <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in RMA6 files"/>
    </xml>

    <token name="@READS_CLI@"><![CDATA[
## Reads  
--paired $reads.paired
--pairedSuffixLength $reads.pairedSuffixLength 
    ]]></token>
    <xml name="reads_macro">
        <section name="reads" title="Reads Options" expanded="true">
            <param argument="--paired" type="boolean" truevalue="true" falsevalue="false" checked="false" label="" />
            <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish names" help="i.e. first word in header) of read and its mate (use 0 if read and mate have same name" />
            <yield/>
        </section>
    </xml>

    <token name="@PARAMETERS_CLI@"><![CDATA[
##Parameters  
--longReads $params.longReads
--classify $params.classify
--minScore $params.minScore
--maxExpected $params.maxExpected
--minPercentIdentity $params.minPercentIdentity
--topPercent $params.topPercent
--minSupportPercent $params.minSupportPercent
--minSupport $params.minSupport
--minPercentReadCover $params.minPercentReadCover
--minPercentReferenceCover $params.minPercentReferenceCover
--lcaAlgorithm $params.lcaAlgorithm
--lcaCoveragePercent $params.lcaCoveragePercent
--readAssignmentMode $params.readAssignmentMode
#if $params.conFile:
    --conFile '$params.conFile'
#end if
    ]]></token>
    <xml name="params_macro">
        <section name="params" title="Parameters" expanded="true">
            <param argument="--longReads" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Parse and analyse as long reads" />
            <yield/>
            <param argument="--classify" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run classification algorithm" />
            <param argument="--minScore" type="float" value="50.0" label="Min score" />
            <param argument="--maxExpected" type="float" value="0.01" label="Max expected" />
            <param argument="--minPercentIdentity" type="float" value="0.00" label="Min percent identity" />
            <param argument="--topPercent" type="float" value="10.0" label="Top percent" />
            <param argument="--minSupportPercent" type="float" value="0.05" label="Min support as percent of assigned reads (0==off)" />
            <param argument="--minSupport" type="integer" value="0" label="Min support (0==off)" />
            <param argument="--minPercentReadCover" type="float" value="0.0" label="Min percent of read length to be covered by alignments" />
            <param argument="--minPercentReferenceCover" type="float" value="0.0" label="Min percent of reference length to be covered by alignments" />
            <param argument="--lcaAlgorithm" type="select" label="LCA algorithm to use for taxonomic assignment">
                <option value="naive" selected="true">naive</option>
                <option value="weighted">weighted</option>
                <option value="longReads">longReads</option>
            </param>
            <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Set the percent for the LCA to cover" />
            <param argument="--readAssignmentMode" type="select" label="Read assignment mode">
                <option value="readCount" selected="true">readCount</option>
                <option value="readLength">readLength</option>
                <option value="alignedBases">alignedBases</option>
                <option value="readMagnitude">readMagnitude</option>
            </param>
            <param argument="--conFile" type="data" format="tabular" optional="true" label="File of contaminant taxa" help="one Id or name per line"/>
        </section>
    </xml>

    <token name="@CLASSIFICATION_CLI@"><![CDATA[
##Classification support:
--parseTaxonNames $classification.parseTaxonNames
#for $cat in $CATEGORIES:
    #for $target in $TARGETS
        $get_mapping_acc_gi( $classification['section_'+$target], $cat, $target )
    #end for
#end for
    ]]></token>
    <xml name="classification_macro">
        <section name="classification" title="Classification support options" expanded="true">
            <param argument="--parseTaxonNames" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Parse taxon names" />

            <expand macro="mappings_gi_acc_syn" target="taxa" targetlabel="Taxonomy"/>
            <expand macro="mappings_gi_acc_syn_tags" target="eggnog" targetlabel="EGGNOG"/>
            <expand macro="mappings_gi_acc_syn_tags" target="interpro2go" targetlabel="INTERPRO2GO"/>
            <expand macro="mappings_gi_acc_syn_tags" target="seed" targetlabel="SEED"/>
            <expand macro="mappings_gi_acc_syn_tags" target="kegg" targetlabel="KEGG"/>
        </section>
    </xml>
    
    <token name="@OTHER_CLI@"><![CDATA[
##Other:
--firstWordIsAccession $other.firstWordIsAccession
#if len($other.accessionTags)>0:
    --accessionTags 
    #for $i, $s in enumerate($other.accessionTags)
        '$s.tag'
    #end for
#end if
    ]]></token>
    <xml name="other_macro">
        <section name="other" title="Other options" expanded="true">
            <param argument="--firstWordIsAccession" type="boolean" truevalue="true" falsevalue="false" checked="true" label="First word in reference header is accession number" help="enable for NCBI-nr downloaded Sep 2016 or later" />
            <repeat name="accessionTags" title="List of accession tags" min="0" default="0" help="Default value(s): gb| ref|.">
                <param name="tag" type="text" label="Accession tag"/>
            </repeat>
        </section>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nmeth.3176</citation>
            <citation type="doi">10.1101/gr.120618.111</citation>
            <citation type="doi">10.1101/gr.5969107</citation>
            <citation type="bibtex">
@misc{website,
  author = {Huson et al},
  year = {TODO},
  title = {Megan Website},
  url = {http://ab.inf.uni-tuebingen.de/software/megan6/},
        }</citation>
        </citations>
    </xml>
</macros>