diff macros.xml @ 6:742c94cfb8cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f

--- a/macros.xml	Wed Feb 27 09:47:34 2019 -0500
+++ b/macros.xml	Thu Jun 20 08:10:32 2019 -0400
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@STACKS_VERSION@">2.3c</token>
+    <token name="@STACKS_VERSION@">2.4</token>
     <token name="@WRAPPER_VERSION@">0</token>
     <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
     <token name="@PROFILE@">18.01</token>
@@ -116,7 +116,7 @@
         #end if
     ]]></token>
     <xml name="in_log">
-        <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
+        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
     </xml>
     <xml name="out_log">
         <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
@@ -138,7 +138,7 @@
         <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />
     </xml>
     <xml name="input_aln_macro">
-        <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
+        <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
     </xml>
 
     <!-- code for creating links to the data sets from previous pipeline steps
@@ -212,7 +212,7 @@
 
     <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
         <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
-            <param name="barcode" argument="-b" type="data"  format="tabular,txt" label="Barcode file" />
+            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
         </expand>
     </xml>
 
@@ -509,6 +509,10 @@
             <filter>populations_output['plink']</filter>
         </data>
 
+		<!--structure populations.hzar-->
+        <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv">
+            <filter>populations_output['hzar']</filter>
+        </data>
         <!--structure populations.structure-->
         <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
             <filter>populations_output['structure']</filter>
@@ -560,9 +564,13 @@
         </expand>
     </xml>
 
-    <!-- variant calling option for use in gstacks and denovomap -->
-    <xml name="variant_calling_options_vg">
-        <param argument="--var-alpha" name="var_alpha" type="float" value="0.01" min="0" label="Alpha threshold for discovering SNPs" />
+	<!-- variant calling option for use in gstacks and denovomap 
+         default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
+         otherwise no default is is available and gstacks will output and error
+         "Error: No value was provided for \-\-var-alpha and there is no default for this model)" 
+	-->
+    <xml name="variant_calling_options_vg" token_varalpha_default="">
+        <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
         <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
     </xml>