diff augustus.xml @ 11:e519d7b4f9ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d

--- a/augustus.xml	Fri May 10 08:25:57 2019 -0400
+++ b/augustus.xml	Thu May 23 18:15:55 2019 -0400
@@ -69,6 +69,13 @@
             $utr
             --genemodel=$genemodel
 
+            #if $hints.usehints == 'T'
+                --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
+            #end if
+
+            #if $range.userange == 'T'
+                --predictionStart=$range.start --predictionEnd=$range.stop
+            #end if
 
             #if $model.augustus_mode == 'history'
                 --species=local
@@ -223,7 +230,7 @@
         </param>
 
         <param name="genemodel" label="Gene Model" type="select"
-            help="Gene Model to predict, for more information please refere to the help.">
+            help="Gene Model to predict, for more information please refer to the help.">
             <option value="complete">complete</option>
             <option value="partial">partial</option>
             <option value="intronless">intronless</option>
@@ -231,6 +238,36 @@
             <option value="exactlyone">exactlyone</option>
         </param>
 
+        <conditional name="hints">
+            <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
+                <option value="F">No</option>
+                <option value="T">Yes</option>
+            </param>
+            <when value="T">
+                <param name="hintsfile" label="Select hints file from history" type="data" format="gff"
+                    help="A file containing hints in gff format (--hintsfile)"/>
+                <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt"
+                    help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/>
+            </when>
+            <when value="F">
+            </when>
+    	</conditional>
+
+        <conditional name="range">
+            <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
+                <option value="F">No</option>
+                <option value="T">Yes</option>
+            </param>
+            <when value="T">
+                <param name="start" label="Starting position" type="integer" value=""
+                    help="The beginning of the search range (--predictionStart)"/>
+                <param name="stop" label="Ending position" type="integer" value=""
+                    help="The end of the search range (--predictionEnd); must be greater than starting position"/>
+            </when>
+            <when value="F">
+            </when>
+        </conditional>
+
         <param name="gff" type="boolean" label="GFF formated output"
             help="Standard output is GTF."
             truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
@@ -279,6 +316,39 @@
             <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
             <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
         </test>
+        <test>
+            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
+            <param name="organism" value="fly" />
+            <param name="usehints" value="T" />
+            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
+            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
+            <param name="outputs" value="" />
+            <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
+                <assert_contents>
+                    <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
+                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
+                </assert_contents>
+            </output>
+
+        </test>
+        <test>
+            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
+            <param name="organism" value="fly" />
+            <param name="usehints" value="T" />
+            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
+            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
+            <param name="userange" value="T" />
+            <param name="start" value="7000" />
+            <param name="stop" value="9000" />
+            <param name="outputs" value="" />
+            <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
+                <assert_contents>
+                    <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
+                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help>
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