From e2ae2c4a75d67db0acc4e9032491236c548ceff3 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Sun, 26 Sep 2010 18:06:01 -0400
Subject: [PATCH] Requirements tags for some samtools tools

---
 tools/samtools/bam_to_sam.xml      | 3 +++
 tools/samtools/pileup_interval.xml | 3 +++
 tools/samtools/sam_merge.xml       | 3 +++
 tools/samtools/sam_pileup.xml      | 3 +++
 tools/samtools/sam_to_bam.xml      | 3 +++
 5 files changed, 15 insertions(+)

diff --git a/tools/samtools/bam_to_sam.xml b/tools/samtools/bam_to_sam.xml
index 7c9a0c199d2..12b5c4ba82f 100644
--- a/tools/samtools/bam_to_sam.xml
+++ b/tools/samtools/bam_to_sam.xml
@@ -1,4 +1,7 @@
 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
   <description>converts BAM format to SAM format</description>
   <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command>
   <inputs>
diff --git a/tools/samtools/pileup_interval.xml b/tools/samtools/pileup_interval.xml
index 808d7070b84..24c045ec6d6 100644
--- a/tools/samtools/pileup_interval.xml
+++ b/tools/samtools/pileup_interval.xml
@@ -1,5 +1,8 @@
 <tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.0">
   <description>condenses pileup format into ranges of bases</description>
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
   <command interpreter="python">
     pileup_interval.py 
       --input=$input 
diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index a0aeab23dbf..ef113befb99 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -1,5 +1,8 @@
 <tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
   <description>merges BAM files together</description>
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
   <command interpreter="python">
    sam_merge.py 
       $input1
diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml
index 0536c8ba8db..2552fa4dfc6 100644
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -1,5 +1,8 @@
 <tool id="sam_pileup" name="Generate pileup" version="1.1.0">
   <description>from BAM dataset</description>
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
   <command interpreter="python">
     sam_pileup.py
         --input1=$input1
diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml
index c9dc90f6292..8e63d46ad25 100644
--- a/tools/samtools/sam_to_bam.xml
+++ b/tools/samtools/sam_to_bam.xml
@@ -1,5 +1,8 @@
 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
   <description>converts SAM format to BAM format</description>
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
   <command interpreter="python">
 sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} 
 #if $source.index_source == "history":