Mercurial > repos > iuc > gtftobed12
diff gtfToBed12.xml @ 0:75a14cc16d4d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit adc4f5c431fca0bcdf93188b7065bdc4c9c424c6
author | iuc |
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date | Fri, 18 May 2018 15:10:34 -0400 |
parents | |
children | 57d45064f114 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtfToBed12.xml Fri May 18 15:10:34 2018 -0400 @@ -0,0 +1,127 @@ +<tool id="gtftobed12" name="Convert GTF to BED12" version="357"> + <requirements> + <requirement type="package" version="357">ucsc-gtftogenepred</requirement> + <requirement type="package" version="357">ucsc-genepredtobed</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + gtfToGenePred + #if $advanced_options.advanced_options_selector == "advanced": + $advanced_options.ignoreGroupsWithoutExons + $advanced_options.simple + $advanced_options.allErrors + $advanced_options.impliedStopAfterCds + $advanced_options.includeVersion + #if $advanced_options.infoOut: + -infoOut='${transcript_info_file}' + #end if + #for $prefix in $advanced_options.sourcePrefixes + -sourcePrefix='${prefix.sourcePrefix}' + #end for + #end if + '${gtf_file}' + 'temp.genePred' && + genePredToBed 'temp.genePred' '${bed_file}' + ]]> + </command> + <inputs> + <param name="gtf_file" type="data" format="gtf" label="GTF File to convert" /> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Advanced options" + help="Advanced options for gtfToGenePred."> + <option value="default" selected="true">Use default options</option> + <option value="advanced">Set advanced options</option> + </param> + <when value="default" /> + <when value="advanced"> + <repeat name="sourcePrefixes" title="Source Prefixes" + help="Only process entries where the source name has the specified prefixes"> + <param argument="-sourcePrefix" label="Source prefix" + type="text" /> + </repeat> + <param argument="-ignoreGroupsWithoutExons" label="Ignore groups without exons" + help="Ignore groups that do not have exons, otherwise they will cause an error." + type="boolean" truevalue="-ignoreGroupsWithoutExons" falsevalue="" checked="false" /> + <param argument="-simple" label="Skip hierarchy check" + help="Only check column validity, not heirarchy, may result in invalid output." + type="boolean" truevalue="-simple" falsevalue="" checked="false" /> + <param argument="-allErrors" label="Skip all errors" + help="Skip groups with errors rather than aborting. Useful for getting information + about as many errors as possible." + type="boolean" truevalue="-allErrors" falsevalue="" checked="false" /> + <param argument="-impliedStopAfterCds" label="Implied stop codon in after CDS" + help="Assume there is an implied stop codon after CDS." + type="boolean" truevalue="-impliedStopAfterCds" falsevalue="" checked="false" /> + <param argument="-includeVersion" label="Include gene and transcript version" + help="If gene_version and/or transcript_version attributes exist, include the version + in the corresponding identifiers." + type="boolean" truevalue="-includeVersion" falsevalue="" checked="false" /> + <param argument="-infoOut" label="Output transcript information file" + help="Outputs a file with information about each transcript." + type="boolean" checked="false" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="bed_file" format="bed12" metadata_source="gtf_file" /> + <data name="transcript_info_file" format="tabular" metadata_source="gtf_file"> + <filter>advanced_options['infoOut']</filter> + </data> + </outputs> + <tests> + <test> + <param name="gtf_file" value="gtf2bed_test.gtf"/> + <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> + </test> + <test> + <param name="gtf_file" value="gtf2bed_test_missing_exon.gtf"/> + <param name="advanced_options_selector" value="advanced" /> + <param name="ignoreGroupsWithoutExons" value="true" /> + <output name="bed_file" file="gtf2bed_test_missing_exon.bed" ftype="bed12"/> + </test> + <test> + <param name="gtf_file" value="gtf2bed_test.gtf"/> + <param name="advanced_options_selector" value="advanced" /> + <param name="includeVersion" value="true" /> + <output name="bed_file" file="gtf2bed_test_include_version.bed" ftype="bed12"/> + </test> + <test> + <param name="gtf_file" value="gtf2bed_test.gtf"/> + <param name="advanced_options_selector" value="advanced" /> + <param name="infoOut" value="true" /> + <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> + <output name="transcript_info_file" file="gtf2bed_test_transcript_info.txt" ftype="tabular"/> + </test> + <test> + <param name="gtf_file" value="gtf2bed_test.gtf"/> + <param name="advanced_options_selector" value="advanced" /> + <repeat name="sourcePrefixes"> + <param name="sourcePrefix" value="hav" /> + </repeat> + <output name="bed_file" file="gtf2bed_test_havana.bed" ftype="bed12"/> + </test> + <test> + <param name="gtf_file" value="gtf2bed_test.gtf"/> + <param name="advanced_options_selector" value="advanced" /> + <repeat name="sourcePrefixes"> + <param name="sourcePrefix" value="hav" /> + </repeat> + <repeat name="sourcePrefixes"> + <param name="sourcePrefix" value="ens" /> + </repeat> + <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> + </test> + </tests> + <help><![CDATA[ +Converts a GTF_ file to a BED12_ formatted file using UCSC tools from Jim Kent. + +``gtfToGenePred``, followed by ``genePredToBed`` + +.. _GTF: https://genome.ucsc.edu/FAQ/FAQformat.html#format4 +.. _BED12: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 + ]]> + </help> + + <citations> + <citation type="doi">10.1101/gr.229102</citation> + </citations> +</tool>