diff heatmap.xml @ 1:d8c45afa221c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22

--- a/heatmap.xml	Sun May 14 20:11:11 2023 +0000
+++ b/heatmap.xml	Fri Sep 29 15:43:22 2023 +0000
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="xrefs"/>
+    <expand macro="creators"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[  
         #import re
@@ -11,7 +12,7 @@
         #set $x=1
         #for $x, $file in enumerate($filenames):
             #set $name_base = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
-            #set $name = $name_base + '_' + str(x)
+            #set $name = $name_base
             #silent $names.append( $name )
             ln -s '$file' ${name}.cns  &&
         #end for
@@ -42,7 +43,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="filenames" multiple="true" type="data" format="cns" label="cns sample file" help="Sample coverages as raw probes cnr or segments cns)" />
+        <param name="filenames" multiple="true" type="data" format="tabular" label="CN segmentation calls cns file/s" help="Sample coverages as raw probes cnr or segments cns" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
             <expand macro="heatmap_optional" />
             <expand macro="sample_sex_condition" />
@@ -54,7 +55,6 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
-            <param name="by_bin" value="1" />
             <param name="desaturate" value="1" />
             <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
                 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
@@ -62,10 +62,9 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="Sample_sex">
-                <param name="sex" value="yes" />
+                <param name="sex" value="no" />
             </conditional>
             <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
-            <param name="by_bin" value="1" />
             <param name="desaturate" value="1" />
             <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
                 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>