# HG changeset patch
# User devteam
# Date 1393002378 18000
# Node ID 93ace7e49295b999738d5e40042408ec91ac8c76
# Parent  ab5e8beab4fe5053f225a92a97d6ff53c9b9c09b
Uploaded valid tools.

diff -r ab5e8beab4fe -r 93ace7e49295 rgPicardASMetrics.xml
--- a/rgPicardASMetrics.xml	Tue Dec 17 16:12:31 2013 -0500
+++ b/rgPicardASMetrics.xml	Fri Feb 21 12:06:18 2014 -0500
@@ -1,10 +1,10 @@
 <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
   <command interpreter="python">
-    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
-    --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext"
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
+    --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}"
     -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar  --tmpdir "${__new_file_path__}" 
 #if $genomeSource.refGenomeSource == "history":
-    --ref-file "$genomeSource.ownFile"
+    --ref-file "${genomeSource.ownFile}"
 #else
     --ref "${genomeSource.index.fields.path}"
 #end if
@@ -26,7 +26,7 @@
       <when value="default">
         <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
           <options from_data_table="all_fasta">
-          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator="," />
+          <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator="," />
           <validator type="no_options" message="No reference build available for selected input" /> 
           </options>
         </param>
diff -r ab5e8beab4fe -r 93ace7e49295 rgPicardGCBiasMetrics.xml
--- a/rgPicardGCBiasMetrics.xml	Tue Dec 17 16:12:31 2013 -0500
+++ b/rgPicardGCBiasMetrics.xml	Fri Feb 21 12:06:18 2014 -0500
@@ -1,8 +1,8 @@
 <tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0">
   <command interpreter="python">
-    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
-    --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
-    -j \$JAVA_JAR_PATH/CollectGcBiasMetrics.jar
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
+    --windowsize "${windowsize}" --mingenomefrac "${mingenomefrac}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
+    -j "\$JAVA_JAR_PATH/CollectGcBiasMetrics.jar"
 #if $genomeSource.refGenomeSource == "history":
  --ref-file "${genomeSource.ownFile}"
 #else:
@@ -24,7 +24,7 @@
       <when value="default">
         <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
           <options from_data_table="all_fasta">
-          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/>
+          <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator=","/>
           <validator type="no_options" message="No reference build available for the selected input data" />
           </options>
         </param>