Mercurial > repos > iuc > cnvkit_export_jtv

diff jtv.xml @ 0:d30f7b4c0722 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:45:00 +0000
parents
children 6617cb1fcbcc
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jtv.xml	Mon Jan 20 16:45:00 2025 +0000
@@ -0,0 +1,32 @@
+<tool id="cnvkit_export_jtv" name="CNVkit Export JTV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Convert log2 ratios to Java TreeView's native format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_segmented_file' ./sample.cnr &&
+        cnvkit.py export jtv
+            ./sample.cnr
+            --output sample.cnv.jtv
+    ]]></command>
+     <inputs>
+        <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
+        </inputs>
+    <outputs>
+        <data name="CNVs_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
+            <output name="CNVs_cdt" file="sample.cnv.jtv" />
+        </test>
+    </tests>
+    <help><![CDATA[ 
+        This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv), 
+        enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration.
+    ]]></help>
+    <expand macro="citations" />
+</tool>