diff control_freec.xml @ 2:f923c54a17ee draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"

--- a/control_freec.xml	Tue Aug 18 08:52:45 2020 -0400
+++ b/control_freec.xml	Sat Nov 13 18:28:40 2021 +0000
@@ -1,12 +1,10 @@
-<tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
+<tool id="control_freec" name="Control-FREEC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>detects copy-number changes and allelic imbalances</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="5.0.1">gawk</requirement>
-        <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
-    </requirements>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #if str($reference_source.ref_selector) == 'history':
             ln -s '$reference_source.ref' ./genome.fa &&
@@ -30,7 +28,7 @@
         awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&
 
         ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
-        #if $input_control_file
+        #if $WGS_WES.input_control_file
             ln -s '$WGS_WES.input_control_file' ./control.bam &&
         #end if
 
@@ -97,9 +95,11 @@
 mateOrientation = $WGS_WES.mateOrientation_selector
 
 [control]
+#if $WGS_WES.input_control_file
 mateFile = control.bam
 inputFormat = BAM
 mateOrientation = $WGS_WES.mateOrientation_selector
+#end if
 
 #if int($WGS_WES.advanced_settings.window_section.window) == 0
 [target]
@@ -115,7 +115,7 @@
                 <option value="other">other method</option>
             </param>
             <when value="WGS">
-                <expand macro="def_input_files" />
+                <expand macro="wgs_input_files" />
                 <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
                     <expand macro="WGS" />
                     <expand macro="shared" />
@@ -141,7 +141,9 @@
     </inputs>
     <outputs>
         <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
-        <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" />
+        <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn">
+            <filter>WGS_WES['input_control_file']</filter>
+        </data>
         <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
         <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
         <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
@@ -257,6 +259,23 @@
             </output>
             <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
         </test>
+        <!-- Test without control file-->
+        <test expect_num_outputs="4">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="history"/>
+                <param name="ref" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <param name="WGS_WES_selector" value="WGS" />
+            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+            <param name="mateOrientation_selector" value="0" />
+            <param name="minimalSubclonePresence" value="100" />
+            <param name="window" value="50" />
+            <param name="step" value="10" />
+            <output name="out_sample_raw" file="output/sample.bam_sample_woc.cpn" />
+            <output name="out_sample_coord" file="output/sample_woc.bam_CNVs" />
+            <output name="out_sample_info" file="output/sample.bam_info_woc.txt" />
+            <output name="out_sample_ratio" file="output/sample.bam_ratio_woc.txt" />
+        </test>
     </tests>
     <help><![CDATA[
 Control-FREEC