diff segmetrics.xml @ 0:d9cb65e1f756 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/segmetrics.xml	Fri Sep 29 15:39:32 2023 +0000
@@ -0,0 +1,69 @@
+<tool id="cnvkit_segmetrics" name="CNVkit Segmetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>calculate summary statistics</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 &&
+       #if $segments
+            ln -s '$segments' ./sample.cns &&
+       #end if
+       cnvkit.py segmetrics
+            ./sample.cnr              
+            --output gene_segmetrics.cns   
+            #if $segments
+                --segments ./sample.cns
+            #end if                
+            $advanced_settings.mean
+            $advanced_settings.median
+            $advanced_settings.mode
+            $advanced_settings.ttest
+            $advanced_settings.stdev
+            $advanced_settings.sem
+            $advanced_settings.mad
+            $advanced_settings.mse
+            $advanced_settings.iqr
+            $advanced_settings.bivar
+            $advanced_settings.ci
+            $advanced_settings.pi
+            $advanced_settings.alpha
+            $advanced_settings.bootstrap                   
+    ]]></command>
+    <inputs>
+        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnn/cnr file" help="" />
+        <param argument="--segments" optional="true" type="data" format="tabular" label="CN segmentation calls cns file" help="" />  
+        <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
+        <section name="advanced_settings" title="Statistical settings" expanded="false">
+            <expand macro="genemetrics_segmetrics_statistics" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="gene_segmetrics" format="tabular" label="${tool.name} on ${on_string}: bin-level log2 ratio" from_work_dir="gene_segmetrics.cns" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
+            <param name="segments" ftype="tabular" value="sample.cns" />
+            <param name="drop_low_coverage" value="1" />
+            <param name="mean" value="1" />
+            <param name="median" value="1" />
+            <param name="mode" value="0" />
+            <output name="gene_segmetrics">
+                <assert_contents><has_text text="chromosome"/></assert_contents>
+            </output> 
+        </test>
+    </tests>
+    <help><![CDATA[
+        Calculate summary statistics of the residual bin-level log2 ratio estimates from the segment means, similar to 
+        the existing metrics command, but for each segment individually. Results are output in the same format as the 
+        CNVkit segmentation file (.cns), with the stat names and calculated values printed in additional columns.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+
+
+