diff samtools_mpileup.xml @ 13:9da0311ab1dd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 1354b1358df89a922c3243f7e27ce789094b8644"

--- a/samtools_mpileup.xml	Sat Nov 27 12:32:35 2021 +0000
+++ b/samtools_mpileup.xml	Sun Dec 19 15:57:35 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.5" profile="@PROFILE@">
+<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.6" profile="@PROFILE@">
     <description>multi-way pileup of variants</description>
     <macros>
         <import>macros.xml</import>
@@ -37,7 +37,7 @@
         #end if
 
         #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
-            -G '$excluded_read_groups'
+            -G '$$advanced_options.exclude_read_group.group_paste'
         #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
             -G '$advanced_options.exclude_read_group.read_groups'
         #end if
@@ -69,21 +69,21 @@
         <expand macro="mandatory_reference" argument="-f"/>
         <conditional name="advanced_options">
             <param name="advanced_options_selector" type="select" label="Set advanced options">
-                <option selected="True" value="default">Basic</option>
+                <option selected="true" value="default">Basic</option>
                 <option value="advanced">Advanced</option>
             </param>
             <when value="default" />
             <when value="advanced">
                 <conditional name="filter_by_flags">
                     <param name="filter_flags" type="select" label="Set filter by flags">
-                        <option selected="True" value="nofilter">Do not filter</option>
+                        <option selected="true" value="nofilter">Do not filter</option>
                         <option value="filter">Filter by flags to exclude or require</option>
                     </param>
                     <when value="filter">
-                        <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="True" display="checkboxes" label="Require">
+                        <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="true" display="checkboxes" label="Require">
                             <expand  macro="flag_options" />
                         </param>
-                        <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude">
+                        <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="true" display="checkboxes" label="Exclude">
                             <expand  macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
                         </param>
                     </when>
@@ -91,7 +91,7 @@
                 </conditional>
                 <conditional name="limit_by_region">
                     <param name="limit_by_regions" type="select" label="Select regions to call">
-                        <option selected="True" value="no_limit">Do not limit</option>
+                        <option selected="true" value="no_limit">Do not limit</option>
                         <option value="limit">Specify regions</option>
                     </param>
                     <when value="limit">
@@ -106,7 +106,7 @@
 
                 <conditional name="exclude_read_group">
                     <param name="exclude_read_groups" argument="-R/--exclude-RG" type="select" label="Select read groups to exclude">
-                        <option selected="True" value="no_limit">Do not exclude</option>
+                        <option selected="true" value="no_limit">Do not exclude</option>
                         <option value="history">From a text file</option>
                         <option value="paste">Paste a list of read groups</option>
                     </param>
@@ -133,7 +133,7 @@
         </conditional>
         <conditional name="output_options_cond">
             <param name="output_options_selector" type="select" label="Output options">
-                <option selected="True" value="default">Default</option>
+                <option selected="true" value="default">Default</option>
                 <option value="advanced">Advanced</option>
             </param>
             <when value="default"/>
@@ -142,7 +142,7 @@
                 <param name="output_mapping_quality" argument="-s/--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
                 <param name="output_read_names" argument="--output-QNAME" type="boolean" truevalue="--output-QNAME" falsevalue="" checked="False" label="Output an extra column containing comma-separated read names. (--output-QNAME)" />
                 <param name="output_all_pos" argument="-a" type="select" label="Output absolutely all positions" help="Output all positions, including those with zero depth. (-a) Output absolutely all positions, including unused reference sequences (-aa). Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.">
-                    <option selected="True" value="">No</option>
+                    <option selected="true" value="">No</option>
                     <option value="-a">all (including those with zero depth)</option>
                     <option value="-aa">absolutely all (including unused reference sequences)</option>
                 </param>