Mercurial > repos > matthias > daa2rma
changeset 0:2ac9f9b9dd63 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
| author | matthias |
|---|---|
| date | Mon, 05 Nov 2018 03:40:10 -0500 |
| parents | |
| children | c15cfe82054a |
| files | daa2rma.xml macros.xml test-data/diamond_results.daa test-data/diamond_results.rma test-data/diamond_results_meganized.daa test-data/xyz test-data/xyz.daa |
| diffstat | 7 files changed, 287 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/daa2rma.xml Mon Nov 05 03:40:10 2018 -0500 @@ -0,0 +1,64 @@ +<tool id="daa2rma" name="daa2rma" version="2.2.4"> + <description>Compute a MEGAN rma6 file from a DIAMOND daa file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ +@CLASSIFICATION_UTILS@ + +#set CATEGORIES=['gi2', 'acc2', 'syn2', 'tags4'] +#set TARGETS=['taxa', 'eggnog', 'interpro2go', 'seed', 'kegg'] + +ln -s $in input.daa && +daa2rma +-i input.daa +-o '$rma' + +@MDF_CLI@ +@READS_CLI@ +--pairedReadsInOneFile $reads.pairedReadsInOneFile +@PARAMETERS_CLI@ +--maxMatchesPerRead $params.maxMatchesPerRead +@CLASSIFICATION_CLI@ +@OTHER_CLI@ + ]]></command> + <inputs> + <param argument="--in" type="data" format="daa" label="Input DAA file"/> + <expand macro="mdf_macro"/> + <expand macro="reads_macro"> + <param argument="--pairedReadsInOneFile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Paired reads in one file" help="usually they are in two" /> + </expand> + <expand macro="params_macro"> + <param argument="--maxMatchesPerRead" type="integer" value="100" label="Max matches per read" /> + </expand> + <expand macro="classification_macro"/> + <expand macro="other_macro"/> + </inputs> + <outputs> + <data name="rma" format="rma6" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="in" ftype="daa" value="diamond_results.daa"/> + <output name="rma" ftype="rma6" value="diamond_results.rma" /> + </test> + </tests> + <help><![CDATA[ +Compute a MEGAN RMA6 file from a DIAMOND DAA file + +**Input** + +- DAA file +- metadata mapping file (as defined in http://qiime.org/documentation/file_formats.html +- BIOM 1 format (see http://biom-format.org/documentation/format-versions/biom-1.0.html + +**Output** + +- RMA6 file + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Nov 05 03:40:10 2018 -0500 @@ -0,0 +1,223 @@ +<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"/> + </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>