diff bcftools_stats.xml @ 5:3afcc6474c79 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

--- a/bcftools_stats.xml	Sat Mar 11 18:05:39 2017 -0500
+++ b/bcftools_stats.xml	Thu Apr 13 17:43:15 2017 -0400
@@ -6,7 +6,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.3.1">samtools</requirement>
+        <expand macro="samtools_requirement"/>
+        <requirement type="package" version="2.0.0">matplotlib</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
@@ -14,6 +15,7 @@
 @PREPARE_INPUT_FILES@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
 ## Stats section
 #set $section = $sec_default
 @PREPARE_FASTA_REF@
@@ -32,6 +34,14 @@
 #if $section.user_tstv:
   --user-tstv "${section.user_tstv}"
 #end if
+#if $section.afbins.afbins_select == 'af_bins_list':
+  --af-bins $section.afbins.af_bins_list
+#elif $section.afbins.afbins_select == 'af_bins_file':
+  --af-bins $section.afbins.af_bins_file
+#end if
+#if $section.af_tag:
+  --af-tag "${section.af_tag}"
+#end if
 #if len($input_vcfs) == 1:
 ${section.split_by_ID}
 #end if
@@ -89,7 +99,25 @@
             <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 
                    help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
                   <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
-
+            </param>
+            <conditional name="afbins">
+                <param name="afbins_select" type="select" label="Set af-bins">
+                    <option value="default">use default</option>
+                    <option value="af_bins_list">enter bins</option>
+                    <option value="af_bins_file">read bins from file</option>
+                </param>
+                <when value="default"/>
+                <when value="af_bins_list">
+                    <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)"> 
+                        <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
+                    </param>
+                </when>
+                <when value="af_bins_file">
+                    <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/> 
+                </when>
+            </conditional>
+            <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT">
+                  <validator type="regex" message="TAG">^\w*$</validator>
             </param>
             <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 
                    help="Produce verbose per-site and per-sample output" />