diff crossmap_gff.xml @ 0:5773a57e91e6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crossmap_gff.xml	Tue Sep 26 05:44:21 2017 -0400
@@ -0,0 +1,94 @@
+<tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@-0">
+    <description>Convert genome coordinates or annotation files between genome assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        CrossMap.py gff
+            '${chain_source.input_chain}'
+            '${seq_source.input}'
+
+            #if str($include_fails) == "True"
+            >
+            #end if
+
+            '${output}'
+    ]]></command>
+
+    <inputs>
+        <conditional name="seq_source">
+            <expand macro="source" />
+
+            <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')"/>
+    </inputs>
+
+    <outputs>
+        <!-- GTF/GFF3? test... -->
+        <data format="gff" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+    <!-- GFF -->
+        <test>
+            <param name="input_format" value="gff"/>
+            <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="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="True"/>
+
+            <output name="output" file="test_gff_01_output_a__all.gtf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+GFF / GTF
+---------
+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.
+
+    NOTE:
+
+    - 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>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>