diff crossmap_wig.xml @ 0:0e6f675cea09 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_wig.xml	Tue Sep 26 05:45:09 2017 -0400
@@ -0,0 +1,76 @@
+<tool id="crossmap_wig" name="CrossMap Wig" 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[
+
+            #set $input_file = str($seq_source.input)
+
+        CrossMap.py wig
+            '${chain_source.input_chain}'
+            '${input_file}'
+            '${output}'
+
+            && mv '${output}.bw' '${output}'
+            && mv '${output}.sorted.bgr' '${output2}'
+    ]]></command>
+
+    <inputs>
+        <conditional name="seq_source">
+            <expand macro="source" />
+            <when value="cached">
+                <param format="wig" name="input" type="data" label="Wiggle file">
+                    <validator type="unspecified_build"/>
+                    <!-- Gives error in tests
+                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
+                    -->
+                </param>
+            </when>
+            <when value="history">
+                <param format="wig" name="input" type="data" label="Wiggle file"/>
+            </when>
+        </conditional>
+        <expand macro="chain" />
+    </inputs>
+
+    <outputs>
+        <data format="wig" name="output" label="${tool.name} on ${on_string}" />
+        <data format="wig" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
+    </outputs>
+
+    <tests>
+    <!-- WIG - Doesn't understand fixedStep -->
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+
+            <output name="output" file="test_wig_01_output_a.bw"/>
+            <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+Wig
+---
+
+    Input wiggle data can be in variableStep (for data with irregular
+    intervals) or fixedStep (for data with regular intervals). Regardless of
+    the input, the output will always in bedGraph format. bedGraph format is
+    similar to wiggle format and can be converted into BigWig format using UCSC
+    wigToBigWig tool. We export files in bedGraph because it is usually much
+    smaller than file in wiggle format, and more importantly, CrossMap
+    internally transforms wiggle into bedGraph to increase running speed.
+
+Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details
+]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>