diff monorail.xml @ 37:5656cfea6d97 draft

Uploaded

--- a/monorail.xml	Wed Nov 20 00:47:20 2019 +0000
+++ b/monorail.xml	Wed Nov 20 02:42:57 2019 +0000
@@ -17,28 +17,27 @@
     </requirements>
         <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
         <command detect_errors="aggressive"><![CDATA[
-            snakemake --snakefile "$__tool_directory__/Snakefile"
-            -j \${GALAXY_SLOTS:-4} 
-            --config 
+            run_mr_snakemake.sh "$__tool_directory__/Snakefile"
+            \${GALAXY_SLOTS:-4} 
+                    "$index_source.fields.path"
+                    "$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
+                    "."
+                    "./tmp"
+                    "$index_source.fields.name"
                     #if str($singlePaired.sPaired) == "paired_collection"
-                        inputs="$singlePaired.input.forward,$singlePaired.input.reverse"
+                        "$singlePaired.input.forward,$singlePaired.input.reverse"
                         #if $singlePaired.input.forward.is_of_type("fastq.gz"):
-                            compressed=1
+                            "compressed=1"
                         #end if
                     #else
-                        inputs="$singlePaired.input1"
+                        "$singlePaired.input1"
                         #if str($singlePaired.sPaired) == "paired"
                             inputs="$singlePaired.input1,$singlePaired.input2"
                         #end if
                         #if $singlePaired.input1.is_of_type("fastq.gz"):
-                            compressed=1
+                            "compressed=1"
                         #end if
                     #end if
-                    ref="$index_source.fields.path"
-                    exon_bed="$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
-                    genome="$index_source.fields.name"
-                    output="."
-                    temp="./tmp"
     ]]></command>
     <inputs>
  <!-- FASTQ input(s) and options specifically for paired-end data. -->