1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/8271faa173f6/ changeset: 8271faa173f6 user: fubar date: 2011-09-27 06:37:17 summary: Fixes to picard HSmetrics and GCbias tools for warning message appearing in paster.log from a test parameter (maxmem) which is available in the xml wrapper for sites wanting it but is commented out as distributed. Simple solution now requires the test params to be uncommented too where sites want to expose the option affected #: 2 files (-1 bytes)

--- a/tools/picard/rgPicardGCBiasMetrics.xml Mon Sep 26 16:40:16 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue Sep 27 14:37:17 2011 +1000 @@ -1,4 +1,4 @@ -<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.01"> +<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02"><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__}" @@ -64,7 +64,9 @@ </outputs><tests><test> + <!-- Uncomment this if maxheap is enabled above <param name="maxheap" value="8G" /> + --><param name="out_prefix" value="CollectGCBias" /><param name="windowsize" value="100" /><param name="mingenomefrac" value="0.00001" />

--- a/tools/picard/rgPicardHsMetrics.xml Mon Sep 26 16:40:16 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue Sep 27 14:37:17 2011 +1000 @@ -1,4 +1,4 @@ -<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.01"> +<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02"><description>for targeted resequencing data</description><command interpreter="python">

@@ -33,11 +33,13 @@ </outputs><tests><test> + <!-- Uncomment this if maxheap parameter is enabled + <param name="maxheap" value="8G" /> + --><param name="out_prefix" value="HSMetrics" /><param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" /><param name="bait_bed" value="picard_input_bait.bed" /><param name="target_bed" value="picard_input_bait.bed" /> - <param name="maxheap" value="8G" /><output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/></test></tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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