Mercurial > repos > iuc > cnvkit_scatter

diff scatter.xml @ 1:3323a7867128 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:44:52 +0000
parents ec9731970f8b
children
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line diff
--- a/scatter.xml	Sun May 14 20:10:25 2023 +0000
+++ b/scatter.xml	Fri Sep 29 15:44:52 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[  
         ln -s '$input_cnr_file' ./tumor.cnr &&
@@ -18,7 +19,7 @@
         #end if
         cnvkit.py scatter
             ./tumor.cnr
-            --output sample-scatter.png
+            --output sample-scatter.pdf
             #if $advanced_settings.segment
                 --segment ./segment.cns
             #end if
@@ -71,7 +72,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
+        <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
             <expand macro="scatter_optional" />
             <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
@@ -83,14 +84,14 @@
         </section>   
     </inputs>
     <outputs>
-        <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
+        <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
             <param name="zygosity_freq" value="0.25" />
             <param name="by_bin" value="1" />
-            <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
+            <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
                 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
             </output>
         </test>