diff medaka_variant.xml @ 2:ce2bf68a260d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"

--- a/medaka_variant.xml	Thu May 28 02:39:16 2020 -0400
+++ b/medaka_variant.xml	Thu Jun 18 05:08:40 2020 -0400
@@ -22,6 +22,7 @@
 -s $s
 -m $m
 -t \${GALAXY_SLOTS:-4}
+-p
 -b $b
 -N $N
 -P $P
@@ -53,17 +54,18 @@
             <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option>
             <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option>
             <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option>
+            <option value="round_1_phased.vcf">round_1_phased.vcf</option>
             <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option>
             <option value="round_1_vcf" selected="true">round_1.vcf</option>
             <option value="log">Log</option>
         </param>
     </inputs>
     <outputs>
-        <!-- standard -->
+        <!-- standard output-->
         <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf">
             <filter>'round_1_vcf' in out</filter>
         </data>
-        <!-- optional -->
+        <!-- optional output: round 0 -->
         <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf">
             <filter>'round_0_hap_mixed_probs_hdf' in out</filter>
         </data>
@@ -76,7 +78,7 @@
         <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf">
             <filter>'round_0_hap_mixed_unphased_vcf' in out</filter>
         </data>
-        <!-- round 1 -->
+        <!-- optional output: round 1 -->
         <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf">
             <filter>'round_1_hap_1_vcf' in out</filter>
         </data>
@@ -89,9 +91,13 @@
         <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
             <filter>'round_1_hap_2_probs_hdf' in out</filter>
         </data>
+        <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf">
+            <filter>'round_1_phased.vcf' in out</filter>
+        </data>
         <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
             <filter>'round_1_unfiltered_vcf' in out</filter>
         </data>
+        <!-- optional output: log -->
         <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
@@ -141,6 +147,7 @@
 
 **Output**
 
+- round_0_hap_mixed_phased.bam
 - round_0_hap_mixed_phased.vcf
 - round_0_hap_mixed_probs.hdf
 - round_0_hap_mixed_unphased.vcf
@@ -148,8 +155,10 @@
 - round_1_hap_1.vcf
 - round_1_hap_2_probs.hdf
 - round_1_hap_2.vcf
+- round_1_phased.vcf
 - round_1_unfiltered.vcf
 - round_1.vcf
+- log
 
 **References**