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Add picard_FastqToSam.xml and picard_SamToFastq.xml to tool_conf.xml.main.

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Daniel Blankenberg
2011-11-21 08:52:13 -05:00
parent 85e4fe3547
commit 54b4dd64b5
3 changed files with 7 additions and 2 deletions
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tool_conf.xml.main
+3
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@@ -406,6 +406,9 @@
<tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
</section>
<section name="NGS: Picard (beta)" id="picard_beta">
<label text="Conversion" id="picard_conversion"/>
<tool file="picard/picard_FastqToSam.xml" />
<tool file="picard/picard_SamToFastq.xml" />
<label text="QC/Metrics for sam/bam" id="qcsambam"/>
<tool file="picard/picard_BamIndexStats.xml" />
<tool file="picard/rgPicardASMetrics.xml" />
tools/picard/picard_FastqToSam.xml
+2 -1
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@@ -1,6 +1,7 @@
<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
<description>creates an unaligned BAM file</description>
<requirements><requirement type="package">picard</requirement></requirements>
<requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
<!-- Dan Blankenberg -->
<command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
FASTQ="${input_fastq1}"
tools/picard/picard_SamToFastq.xml
+2 -1
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@@ -1,6 +1,7 @@
<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0">
<description>creates a FASTQ file</description>
<requirements><requirement type="package">picard</requirement></requirements>
<requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
<!-- Dan Blankenberg -->
<command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
INPUT="${input_sam}"