# HG changeset patch
# User devteam <devteam@galaxyproject.org>
# Date 1364910156 14400
# Node ID 9227b8c3093b25ed5b1b19208e4d16ef5549e183
# Parent  e0232cbac965730424d45400be67a7ff4ddc95e5
Updated command line format per dev team standards.

diff -r e0232cbac965 -r 9227b8c3093b picard_AddOrReplaceReadGroups.xml
--- a/picard_AddOrReplaceReadGroups.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_AddOrReplaceReadGroups.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,19 +2,19 @@
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input="$inputFile"
-      --rg-lb="$rglb"
-      --rg-pl="$rgpl"
-      --rg-pu="$rgpu"
-      --rg-sm="$rgsm"
-      --rg-id="$rgid"
-      --rg-opts=${readGroupOpts.rgOpts}
+      --input="${inputFile}"
+      --rg-lb="${rglb}"
+      --rg-pl="${rgpl}"
+      --rg-pu="${rgpu}"
+      --rg-sm="${rgsm}"
+      --rg-id="${rgid}"
+      --rg-opts="${readGroupOpts.rgOpts}"
       #if $readGroupOpts.rgOpts == "full"
-        --rg-cn="$readGroupOpts.rgcn"
-        --rg-ds="$readGroupOpts.rgds"
+        --rg-cn="${readGroupOpts.rgcn}"
+        --rg-ds="${readGroupOpts.rgds}"
       #end if
-      --output-format=$outputFormat
-      --output=$outFile
+      --output-format="${outputFormat}"
+      --output="${outFile}"
       -j "\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar"
       --tmpdir "${__new_file_path__}" 
   </command>
diff -r e0232cbac965 -r 9227b8c3093b picard_BamIndexStats.xml
--- a/picard_BamIndexStats.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_BamIndexStats.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,10 +2,10 @@
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input "$input_file"
-      --bai-file "$input_file.metadata.bam_index"
-      -t "$htmlfile"
-      -d "$htmlfile.files_path"
+      --input "${input_file}"
+      --bai-file "${input_file.metadata.bam_index}"
+      -t "${htmlfile}"
+      -d "${htmlfile.files_path}"
       -j "\$JAVA_JAR_PATH/BamIndexStats.jar"
       --tmpdir "${__new_file_path__}" 
   </command>
diff -r e0232cbac965 -r 9227b8c3093b picard_ReorderSam.xml
--- a/picard_ReorderSam.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_ReorderSam.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,19 +2,19 @@
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input=$inputFile
+      --input="${inputFile}"
       #if $source.indexSource == "built-in"
         --ref="${source.ref.fields.path}"
       #else
-        --ref-file=$refFile
-        --species-name=$source.speciesName
-        --build-name=$source.buildName
-        --trunc-names=$source.truncateSeqNames
+        --ref-file="${refFile}"
+        --species-name="${source.speciesName}"
+        --build-name="${source.buildName}"
+        --trunc-names="${source.truncateSeqNames}"
       #end if
-      --allow-inc-dict-concord=$allowIncDictConcord
-      --allow-contig-len-discord=$allowContigLenDiscord
-      --output-format=$outputFormat
-      --output=$outFile
+      --allow-inc-dict-concord="${allowIncDictConcord}"
+      --allow-contig-len-discord="${allowContigLenDiscord}"
+      --output-format="${outputFormat}"
+      --output="${outFile}"
       --tmpdir "${__new_file_path__}" 
       -j "\$JAVA_JAR_PATH/ReorderSam.jar"
   </command>
diff -r e0232cbac965 -r 9227b8c3093b picard_ReplaceSamHeader.xml
--- a/picard_ReplaceSamHeader.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_ReplaceSamHeader.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,10 +2,10 @@
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input "$inputFile"
-      -o $outFile
-      --header-file $headerFile
-      --output-format $outputFormat
+      --input "${inputFile}"
+      -o "${outFile}"
+      --header-file "${headerFile}"
+      --output-format "${outputFormat}"
       -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
       --tmpdir "${__new_file_path__}" 
   </command>
diff -r e0232cbac965 -r 9227b8c3093b picard_SamToFastq.xml
--- a/picard_SamToFastq.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_SamToFastq.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -8,8 +8,8 @@
     -jar "\$JAVA_JAR_PATH/SamToFastq.jar"
     INPUT="${input_sam}"
     VALIDATION_STRINGENCY="LENIENT"
-    RE_REVERSE=${re_reverse}
-    INCLUDE_NON_PF_READS=${include_non_pf_reads}
+    RE_REVERSE="${re_reverse}"
+    INCLUDE_NON_PF_READS="${include_non_pf_reads}"
     #if str( $clipping_attribute ):
         CLIPPING_ATTRIBUTE="${clipping_attribute}"
     #end if
@@ -22,7 +22,7 @@
     #if str( $read1_max_bases_to_write ):
         READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
     #end if
-    INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments}
+    INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
     
     #if str( $output_per_read_group_selector ) == 'per_sam_file':
         ##OUTPUT_PER_RG=false
@@ -54,7 +54,7 @@
         #end if
         '
         --read_group_file_1 "${output_fastq1}"
-        --new_files_path "${$__new_file_path__}"
+        --new_files_path "${__new_file_path__}"
         --file_id_1 "${output_fastq1.id}"
     #end if
   </command>
diff -r e0232cbac965 -r 9227b8c3093b rgPicardASMetrics.xml
--- a/rgPicardASMetrics.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardASMetrics.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -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
diff -r e0232cbac965 -r 9227b8c3093b rgPicardFixMate.xml
--- a/rgPicardFixMate.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardFixMate.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -1,8 +1,8 @@
 <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0">
   <description>for paired data</description>
   <command interpreter="python">
-   picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" 
-   --output-format "$outputFormat" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "$sortOrder"
+   picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" 
+   --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}"
   </command>
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <inputs>
diff -r e0232cbac965 -r 9227b8c3093b rgPicardGCBiasMetrics.xml
--- a/rgPicardGCBiasMetrics.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardGCBiasMetrics.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -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:
diff -r e0232cbac965 -r 9227b8c3093b rgPicardHsMetrics.xml
--- a/rgPicardHsMetrics.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardHsMetrics.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,8 +2,8 @@
   <description>for targeted resequencing data</description>
   <command interpreter="python">
 
-    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext"
-    --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}"
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}"
+    --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
     -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar"
 
   </command>
diff -r e0232cbac965 -r 9227b8c3093b rgPicardInsertSize.xml
--- a/rgPicardInsertSize.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardInsertSize.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,9 +2,9 @@
   <description>for PAIRED data</description>
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
-   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
-   --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
-   -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}"
+   --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}"
+   -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}"
   </command>
   <inputs>
     <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
diff -r e0232cbac965 -r 9227b8c3093b rgPicardLibComplexity.xml
--- a/rgPicardLibComplexity.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardLibComplexity.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -1,9 +1,9 @@
 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
-   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
-   --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
-   -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}"
+   --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
+   -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}"
   </command>
   <inputs>
     <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
diff -r e0232cbac965 -r 9227b8c3093b rgPicardMarkDups.xml
--- a/rgPicardMarkDups.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardMarkDups.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -1,8 +1,8 @@
 <tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0">
   <command interpreter="python">
-   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file"
-   --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist"
-   -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext"
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}"
+   --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
+   -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}"
   </command>
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <inputs>