changeset 1:92cdc29a8620 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

--- a/macros.xml	Sat May 23 13:37:48 2020 -0400
+++ b/macros.xml	Thu May 28 02:39:16 2020 -0400
@@ -22,20 +22,20 @@
         </citations>
     </xml>
 
-    <!-- 
+    <!--
         command
     -->
 
-    <token name="@REF_FASTA@"><![CDATA[        
+    <token name="@REF_FASTA@"><![CDATA[
         #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' 'reference.fa' &&
+            ln -f -s '$reference_source.ref_file' reference.fa &&
         #else:
-            ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' &&
+            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
         #end if
     ]]></token>
 
     <!--
-        input 
+        input
     -->
 
     <xml name="b" token_argument="-b">

--- a/medaka_variant.xml	Sat May 23 13:37:48 2020 -0400
+++ b/medaka_variant.xml	Thu May 28 02:39:16 2020 -0400
@@ -6,32 +6,32 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        ## initialize
-        @REF_FASTA@  
-        ## link doesn't work
-        cp '${i}' 'alignment.bam' &&
-        cp '${i.metadata.bam_index}' 'alignment.bam.bai' &&
+## initialize
+@REF_FASTA@
+## link doesn't work
+cp '${i}' alignment.bam &&
+cp '${i.metadata.bam_index}' alignment.bam.bai &&
 
-        ## run
-        medaka_variant
-        ## optional
-        #if str($r) != ''
-            -r '$r'
-        #end if
-        -o 'results'
-        -s '$s'
-        -m '$m'
-        -t \${GALAXY_SLOTS:-4}
-        -b $b
-        -N $N
-        -P $P
-        $U
-        $S
-        ## required
-        -i 'alignment.bam'
-        -f 'reference.fa'
+## run
+medaka_variant
+## optional
+#if $r:
+    -r '$r'
+#end if
+-o results
+-s $s
+-m $m
+-t \${GALAXY_SLOTS:-4}
+-b $b
+-N $N
+-P $P
+$U
+$S
+## required
+-i alignment.bam
+-f reference.fa
 
-        |& tee 'log.txt'
+|& tee '$out_log'
     ]]></command>
     <inputs>
         <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
@@ -92,7 +92,7 @@
         <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
             <filter>'round_1_unfiltered_vcf' in out</filter>
         </data>
-        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>

Binary file test-data/variants.vcf.gz has changed

--- a/tool_data_table_conf.xml.sample	Sat May 23 13:37:48 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 28 02:39:16 2020 -0400
@@ -4,4 +4,4 @@
         <columns>value, dbkey, name, path</columns>
         <file path="all_fasta.loc" />
     </table>
-</tables>
\ No newline at end of file
+</tables>