Commits

Daniel Blankenberg committed fd76a44

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

Comments (0)

Files changed (3)

tool_conf.xml.main

       <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

 <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

 <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}"
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