diff crossmap_wig.xml @ 1:81986a56b281 draft

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

--- a/crossmap_wig.xml	Tue Sep 26 05:45:09 2017 -0400
+++ b/crossmap_wig.xml	Fri Oct 20 02:49:58 2017 -0400
@@ -7,51 +7,44 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-
-            #set $input_file = str($seq_source.input)
+CrossMap.py wig
+'${chain_source.input_chain}'
+'${input}'
+'${output}'
 
-        CrossMap.py wig
-            '${chain_source.input_chain}'
-            '${input_file}'
-            '${output}'
-
-            && mv '${output}.bw' '${output}'
-            && mv '${output}.sorted.bgr' '${output2}'
+&& mv '${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>
+        <param name="input" type="data" format="wig" label="Wiggle file"/>
+
         <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 ${on_string}" />
+        <data name="output" format="wig" label="${tool.name} on ${on_string}" />
+        <data name="output2" format="bedgraph" label="${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="index_source" value="history"/>
             <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>
+
+        <test>
+            <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
+            <param name="index_source" value="cached"/>
+
+            <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@
@@ -59,16 +52,15 @@
 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.
+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>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>