diff breaks.xml @ 0:ef9a50eb20ce draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/breaks.xml	Fri Sep 29 15:45:16 2023 +0000
@@ -0,0 +1,52 @@
+<tool id="cnvkit_breaks" name="CNVkit Breaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>List the targeted genes with segmentaion breakpoint</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators_and_zahra"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_filename_file' ./sample.cnr &&
+        ln -s '$input_segment_file' ./sample.cns &&
+        cnvkit.py breaks
+            ./sample.cnr
+            ./sample.cns 
+            --output gene-breaks.txt
+            #if $min_probes
+                --min-probes $min_probes
+            #end if                    
+    ]]></command>
+    <inputs>
+        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
+        <param name="input_segment_file" type="data"  format="tabular" label="CN segmentation calls cnn file" help="The output of the CNVkit segment" />
+        <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />     
+    </inputs>
+    <outputs>
+        <data name="gene_breaks" format="text" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
+            <param name="input_segment_file" ftype="tabular" value="sample.cns" />
+            <param name="min_probes" value="1" />
+            <output name="gene_breaks">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output> 
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+       Identify genes in which: 
+       (I) an unbalanced fusion or other structural rearrangement breakpoint occured
+       (II) CNV calling is simply difficult due to an inconsistent copy number signal
+       
+       The breaks output is a text table of tab-separated values, which is amenable to further processing by 
+       scripts and standard Unix tools such as grep, sort, cut and awk. 
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+
+
+