diff crossmap_gff.xml @ 7:1b57bf1bb4ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5

--- a/crossmap_gff.xml	Tue Sep 26 06:09:26 2017 -0400
+++ b/crossmap_gff.xml	Fri Oct 20 02:48:09 2017 -0400
@@ -8,59 +8,49 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        CrossMap.py gff
-            '${chain_source.input_chain}'
-            '${seq_source.input}'
+CrossMap.py gff
+'${chain_source.input_chain}'
+'${input}'
 
-            #if str($include_fails) == "True"
-            >
-            #end if
+#if str($include_fails) == "True"
+    >
+#end if
 
-            '${output}'
+'${output}'
     ]]></command>
 
     <inputs>
-        <conditional name="seq_source">
-            <expand macro="source" />
+        <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
 
-            <when value="cached">
-                <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
-                    <validator type="unspecified_build"/>
-                    <!-- Gives error in tests
-                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
-                    -->
-                </param>
-            </when>
-            <when value="history">
-                <param type="data" format="gtf,gff,gff3" name="input"       label="GTF/GFF file"/>
-            </when>
-        </conditional>
         <expand macro="chain" />
 
-        <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
+        <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
     </inputs>
 
     <outputs>
-        <!-- GTF/GFF3? test... -->
-        <data format="gff" name="output" label="${tool.name} on ${on_string}" />
+        <data name="output" format="gff" label="${tool.name} on ${on_string}" />
     </outputs>
 
     <tests>
-    <!-- GFF -->
         <test>
-            <param name="input_format" value="gff"/>
+            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="index_source" value="history"/>
-            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="False"/>
 
             <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
         </test>
         <test>
-            <param name="input_format" value="gff"/>
+            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="index_source" value="history"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="True"/>
+
+            <output name="output" file="test_gff_01_output_a__all.gtf"/>
+        </test>
+        <test><!-- cached chain file -->
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
-            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="index_source" value="cached"/>
             <param name="include_fails" value="True"/>
 
             <output name="output" file="test_gff_01_output_a__all.gtf"/>
@@ -73,20 +63,19 @@
 ---------
 Your input data should be either GTF/GFF2.5 or GFF3 format.
 
-    GFF (General Feature Format) is another plain text file used to describe
-    gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
-    first eight fields are the same as GFF. Only chromosome and genome
-    coordinates are updated. The format of output is determined from the input.
+GFF (General Feature Format) is another plain text file used to describe
+gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
+first eight fields are the same as GFF. Only chromosome and genome
+coordinates are updated. The format of output is determined from the input.
 
-    NOTE:
+Notes:
 
-    - Each feature (exon, intron, UTR, etc) is processed separately and
-      independently, and we do NOT check if features originally belonging to
-      the same gene were converted into the same gene.
-    - If user want to liftover gene annotation files, use BED12 format.
+- Each feature (exon, intron, UTR, etc) is processed separately and
+  independently, and we do NOT check if features originally belonging to
+  the same gene were converted into the same gene.
+- If user want to liftover gene annotation files, use BED12 format.
 
-Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details
-]]></help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>