diff macros.xml @ 2:f923c54a17ee draft default tip

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

--- a/macros.xml	Tue Aug 18 08:52:45 2020 -0400
+++ b/macros.xml	Sat Nov 13 18:28:40 2021 +0000
@@ -1,6 +1,12 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@TOOL_VERSION@">11.6</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="5.0.1">gawk</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
+        </requirements>
+    </xml>
     <xml name="reference_interface">
         <conditional name="reference_source">
             <param name="ref_selector" type="select" label="Choose the source for the reference genome">
@@ -20,6 +26,11 @@
             </when>
         </conditional>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">freec</xref>
+        </xrefs>
+    </xml>
     <xml name="WGS">
         <param name="degree" type="select" label="Degree of polynomial" help="">
             <option value="34" selected="True">GC-content based normalization, WGS (3&amp;4)</option>
@@ -115,7 +126,7 @@
             <param name="sex" type="select" label="Sample sex" help="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; will not annotate one copy of chr X and Y as a loss.">
                 <option value="XY" selected="True">XY</option>
                 <option value="XX">XX</option>
-                <option value="no value"></option>
+                <option value="no value">Do not expecify sex</option>
             </param>
             <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." />
             <!-- uniqueMatch if true -> gemMappabilityFile is needed-->
@@ -139,13 +150,17 @@
         <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." />
         <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." />
     </xml>
+    <xml name="input_control_sample_wgs">
+        <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." />
+        <param name="input_control_file" type="data" format="bam" multiple="false" optional="true" label="Control file" help="Control file in .BAM format." />
+    </xml>
     <xml name="wes_input_files">
         <expand macro="input_control_sample" />
         <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." />
         <expand macro="mateOrientation_selector" />
     </xml>
-    <xml name="def_input_files">
-        <expand macro="input_control_sample" />
+    <xml name="wgs_input_files">
+        <expand macro="input_control_sample_wgs" />
         <expand macro="mateOrientation_selector" />
     </xml>
     <xml name="output_section">