diff gtfToBed12.xml @ 0:75a14cc16d4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit adc4f5c431fca0bcdf93188b7065bdc4c9c424c6

--- /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>