Mercurial > repos > iuc > cnvkit_fix

diff fix.xml @ 1:dc0fb5f07231 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 15:42:57 +0000
parents f64acbe71392
children
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--- a/fix.xml	Sun May 14 20:11:33 2023 +0000
+++ b/fix.xml	Fri Sep 29 15:42:57 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_target_file' ./tumor.targetcoverage.cnn &&
@@ -31,9 +32,9 @@
             $no_rmask
     ]]></command>
     <inputs>
-        <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" />
-        <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" />
-        <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" />
+        <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" />
+        <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Sample Antitarget coverage cnn file" help="" />
+        <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
         <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
         <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
         <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
@@ -41,7 +42,7 @@
         <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
     </inputs>
     <outputs>
-        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" />
+        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">