diff batch.xml @ 1:4653aeb60243 draft

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

--- a/batch.xml	Sun May 14 20:10:48 2023 +0000
+++ b/batch.xml	Fri Sep 29 15:39:59 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 '$CNV_reference.input_sample_file' ./tumor.bam &&
@@ -112,35 +113,35 @@
     <outputs>
         <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
         <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
-        <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: rounded absolute scale copy numbers integer (not log2 ratios) " from_work_dir="tumor.call.cns" />
+        <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
         <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
         <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
         <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
         <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
+        <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
+        <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Output Copy Number Reference Profile" from_work_dir="reference.cnn">
+        <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Output Capture Target" from_work_dir="capture.target.bed">
+        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Output Reference Target" from_work_dir="reference.target-tmp.bed">
+        <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
         </data>
-        <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Output Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
+        <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
         </data>
-        <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Output Sample Diagram" from_work_dir="tumor-diagram.pdf">
+        <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
             <filter>output_section['diagram']</filter>
         </data>
-        <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Output Sample Scatter " from_work_dir="tumor-scatter.png">
+        <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
             <filter>output_section['scatter']</filter>
         </data>
     </outputs>