Mercurial > repos > iuc > cnvkit_fix

diff fix.xml @ 5:aa3fa1c29ccf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 12:00:32 +0000
parents dc0fb5f07231
children
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--- a/fix.xml	Mon Jan 20 16:38:49 2025 +0000
+++ b/fix.xml	Sat Mar 01 12:00:32 2025 +0000
@@ -32,23 +32,23 @@
             $no_rmask
     ]]></command>
     <inputs>
-        <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" />
-        <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Sample Antitarget coverage cnn file" help="" />
-        <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
+        <param name="input_target_file" type="data" format="cnn" label="Sample Target coverage cnn file" help="" />
+        <param name="input_antitarget_file" type="data" optional="true" format="cnn" label="Sample Antitarget coverage cnn file" help="" />
+        <param name="input_reference_coverage_file" type="data" optional="true" format="cnn" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
         <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
-        <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
+        <param argument="--sample-id" type="text" label="Sample ID for target/antitarget files" help="Otherwise inferred from file names" />
         <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
         <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
         <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
     </inputs>
     <outputs>
-        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
+        <data name="out_sample_cnr" format="cnr" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
-            <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" />
-            <param name="input_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" />
+            <param name="input_target_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
+            <param name="input_antitarget_file" ftype="cnn" value="tumor.antitargetcoverage.cnn" />
+            <param name="input_reference_coverage_file" ftype="cnn" value="ref-tas.cnn" />
             <param name="no_edge" value="1" />
             <output name="out_sample_cnr">
                 <assert_contents><has_text text="chromosome"/></assert_contents>