From f53cb1d7f13e1ce281e0bf0cdd0c2af16b37a9af Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 25 Apr 2008 19:40:16 +0000
Subject: [PATCH] Added tool dependencies to xml.

---
 tools/extract/liftOver_wrapper.xml                           | 3 +++
 tools/extract/phastOdds/phastOdds_tool.xml                   | 4 ++++
 tools/hyphy/hyphy_nj_tree_wrapper.xml                        | 3 +++
 tools/maf/maf_stats.xml                                      | 3 +++
 tools/metag_tools/blat_wrapper.xml                           | 3 +++
 tools/metag_tools/megablast_wrapper.xml                      | 3 +++
 tools/metag_tools/megablast_xml_parser.xml                   | 5 ++++-
 tools/metag_tools/rmap_wrapper.xml                           | 3 +++
 tools/metag_tools/rmapq_wrapper.xml                          | 3 +++
 tools/metag_tools/short_reads_figure_high_quality_length.xml | 3 +++
 tools/metag_tools/short_reads_figure_score.xml               | 3 +++
 tools/plotting/bar_chart.xml                                 | 4 ++++
 tools/plotting/histogram2.xml                                | 3 +++
 tools/plotting/scatterplot.xml                               | 3 +++
 tools/regVariation/getIndels_2way.xml                        | 5 ++++-
 tools/regVariation/maf_cpg_filter.xml                        | 5 ++++-
 tools/regVariation/quality_filter.xml                        | 5 ++++-
 tools/stats/cor.xml                                          | 3 +++
 tools/stats/grouping.xml                                     | 3 +++
 tools/stats/gsummary.xml                                     | 3 +++
 tools/taxonomy/gi2taxonomy.xml                               | 3 +++
 tools/taxonomy/t2ps_wrapper.xml                              | 3 +++
 tools/taxonomy/t2t_report.xml                                | 5 ++++-
 23 files changed, 76 insertions(+), 5 deletions(-)

diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index be28b2e90a2..4ade57b4e89 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -15,6 +15,9 @@
     <data format="bed" name="out_file1" />
     <data format="bed" name="out_file2" />
   </outputs>
+  <requirements>
+    <requirement type="binary">liftOver</requirement>
+  </requirements>
   <!--
   <tests>
     <test>
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml
index 7a95f6c842b..4eb15200d80 100644
--- a/tools/extract/phastOdds/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_tool.xml
@@ -15,6 +15,10 @@
   <outputs>
     <data format="interval" name="output" metadata_source="input"/>
   </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+    <requirement type="python-module">tables</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
diff --git a/tools/hyphy/hyphy_nj_tree_wrapper.xml b/tools/hyphy/hyphy_nj_tree_wrapper.xml
index c8cf22e1e5a..431e14e9d12 100644
--- a/tools/hyphy/hyphy_nj_tree_wrapper.xml
+++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml
@@ -26,6 +26,9 @@
         <data name="out_file1" format="tabular" />
         <data name="out_file2" format="pdf" />
     </outputs>
+    <requirements>
+      <requirement type="binary">ps2pdf</requirement>
+    </requirements>
     <tests>
       <test>
         <param name="input1" value="cf_maf2fasta.dat"/>
diff --git a/tools/maf/maf_stats.xml b/tools/maf/maf_stats.xml
index 024646463e1..1b74b57c5ae 100644
--- a/tools/maf/maf_stats.xml
+++ b/tools/maf/maf_stats.xml
@@ -40,6 +40,9 @@
   <outputs>
     <data format="interval" name="out_file1" metadata_source="input1"/>
   </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper.xml
index 188539da13e..aa50b3b7bc0 100644
--- a/tools/metag_tools/blat_wrapper.xml
+++ b/tools/metag_tools/blat_wrapper.xml
@@ -27,6 +27,9 @@
 	<outputs>
 		<data name="output1" format="tabular"/>
 	</outputs>
+	<requirements>
+	  <requirement type="binary">blat</requirement>
+	</requirements>
 	<tests>
 		<test>
 		<param name="source_select" value="database" />
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 3d001117e1a..cbbc558d1d6 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -26,6 +26,9 @@
 	<outputs>
 		<data name="output1" format="tabular"/>
 	</outputs>
+	<requirements>
+		<requirement type="binary">megablast</requirement>
+	</requirements>
 	<tests>
 		<test>
 			<param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
diff --git a/tools/metag_tools/megablast_xml_parser.xml b/tools/metag_tools/megablast_xml_parser.xml
index a74512f2238..bf2638c96db 100644
--- a/tools/metag_tools/megablast_xml_parser.xml
+++ b/tools/metag_tools/megablast_xml_parser.xml
@@ -7,6 +7,9 @@
 <outputs>
 	<data name="output1" format="tabular"/>
 </outputs>
+<requirements>
+	<requirement type="python-module">cElementTree</requirement>
+</requirements>
 <tests>
 	<test>
 		<param name="input1" value="megablast_xml_parser_test1.gz" />
@@ -54,4 +57,4 @@ This tool is for users to upload their own megablast xml output and converts to
 
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/metag_tools/rmap_wrapper.xml b/tools/metag_tools/rmap_wrapper.xml
index 03bcc78d5c1..08edab66500 100644
--- a/tools/metag_tools/rmap_wrapper.xml
+++ b/tools/metag_tools/rmap_wrapper.xml
@@ -32,6 +32,9 @@
     <outputs>
         <data name="output1" format="bed"/>
     </outputs>
+    <requirements>
+      <requirement type="binary">rmap</requirement>
+    </requirements>
     <!--     
     <tests>
         <test>
diff --git a/tools/metag_tools/rmapq_wrapper.xml b/tools/metag_tools/rmapq_wrapper.xml
index 7a536a5f2e7..033af8eff57 100644
--- a/tools/metag_tools/rmapq_wrapper.xml
+++ b/tools/metag_tools/rmapq_wrapper.xml
@@ -35,6 +35,9 @@
     <outputs>
         <data name="output1" format="bed"/>
     </outputs>
+    <requirements>
+      <requirement type="binary">rmapq</requirement>
+    </requirements>
     <!-- 
     <tests>
         <test>
diff --git a/tools/metag_tools/short_reads_figure_high_quality_length.xml b/tools/metag_tools/short_reads_figure_high_quality_length.xml
index 3d99e0f6899..407f225dd71 100644
--- a/tools/metag_tools/short_reads_figure_high_quality_length.xml
+++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml
@@ -12,6 +12,9 @@
 <outputs>
   	<data name="output1" format="pdf" />
 </outputs>
+<requirements>
+	<requirement type="python-module">rpy</requirement>
+</requirements>
 <tests>
 	<test>
 		<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml
index 6e95b43bf38..237b7c079a7 100644
--- a/tools/metag_tools/short_reads_figure_score.xml
+++ b/tools/metag_tools/short_reads_figure_score.xml
@@ -12,6 +12,9 @@
 <outputs>
   	<data name="output1" format="pdf" />
 </outputs> 
+<requirements>
+	<requirement type="python-module">rpy</requirement>
+</requirements>
 <tests>
 	<test>
 		<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
diff --git a/tools/plotting/bar_chart.xml b/tools/plotting/bar_chart.xml
index 4c663eed670..7fd81a7639b 100644
--- a/tools/plotting/bar_chart.xml
+++ b/tools/plotting/bar_chart.xml
@@ -35,6 +35,10 @@
   <outputs>
     <data format="pdf" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="python-module">Gnuplot</requirement>
+    <requirement type="python-module">Numeric</requirement>
+  </requirements>
   <help>
 
 **What it does**
diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram2.xml
index 1b4529a5cb6..0a210c82a49 100644
--- a/tools/plotting/histogram2.xml
+++ b/tools/plotting/histogram2.xml
@@ -23,6 +23,9 @@
       <output name="out_file1" file="histogram_out1.pdf" />
     </test>
   </tests>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
   <help>
 
 .. class:: infomark
diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml
index 285cc0b73e6..32b903bc31c 100644
--- a/tools/plotting/scatterplot.xml
+++ b/tools/plotting/scatterplot.xml
@@ -12,6 +12,9 @@
   <outputs>
     <data format="pdf" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
   <!-- TODO: uncomment the following test when we have tools.update_state() working for 
        multiple dependents with the same dependency.
   <tests>
diff --git a/tools/regVariation/getIndels_2way.xml b/tools/regVariation/getIndels_2way.xml
index 9fcb12b34c6..1d4780ce49a 100644
--- a/tools/regVariation/getIndels_2way.xml
+++ b/tools/regVariation/getIndels_2way.xml
@@ -11,6 +11,9 @@
   <outputs>
     <data format="tabular" name="out_file1" metadata_source="input1"/>
   </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input1" value="6.maf"/>
@@ -53,4 +56,4 @@ Any block/s not containing exactly 2 species will be omitted.
 </help>  
 
 
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/regVariation/maf_cpg_filter.xml b/tools/regVariation/maf_cpg_filter.xml
index 5ee53488c4f..e6bc805bca6 100644
--- a/tools/regVariation/maf_cpg_filter.xml
+++ b/tools/regVariation/maf_cpg_filter.xml
@@ -26,6 +26,9 @@
   <outputs>
     <data format="maf" name="out_file1" metadata_source="input"/>
   </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input" value="6.maf"/>
@@ -59,4 +62,4 @@ For more information on CpG site definitions, please refer this article_.
   </help>  
 
 
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/regVariation/quality_filter.xml b/tools/regVariation/quality_filter.xml
index 67226cb78ca..e1f617ef26b 100644
--- a/tools/regVariation/quality_filter.xml
+++ b/tools/regVariation/quality_filter.xml
@@ -62,6 +62,9 @@
   <outputs>
     <data format="maf" name="out_file1" metadata_source="input"/>
   </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input" value="6.maf"/>
@@ -109,4 +112,4 @@ Also, any primary species whose quality scores are not available in galaxy, will
    
    where, the positions containing # represent panTro2 nucleotides having quality scores less than 20.
   </help>  
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml
index f12d3ff6df9..1458a8dd39f 100644
--- a/tools/stats/cor.xml
+++ b/tools/stats/cor.xml
@@ -13,6 +13,9 @@
   <outputs>
     <data format="txt" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
   <tests>
     <!--
     Test a tabular input with the first line being a comment without a # character to start
diff --git a/tools/stats/grouping.xml b/tools/stats/grouping.xml
index 5f53131d36f..b2c0b1f8fb4 100644
--- a/tools/stats/grouping.xml
+++ b/tools/stats/grouping.xml
@@ -34,6 +34,9 @@
   <outputs>
     <data format="input" name="out_file1" metadata_source="input1" />
   </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
   <tests>
   	<!-- Test valid data -->
   	<!-- Testing this tool will not be possible unless / until the twill team inplements an
diff --git a/tools/stats/gsummary.xml b/tools/stats/gsummary.xml
index 35d5ea457bb..2ab33d39266 100644
--- a/tools/stats/gsummary.xml
+++ b/tools/stats/gsummary.xml
@@ -10,6 +10,9 @@
   <outputs>
     <data format="tabular" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input" value="1.bed"/>
diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml
index c3bc98d4e44..0dc36dd8f8f 100644
--- a/tools/taxonomy/gi2taxonomy.xml
+++ b/tools/taxonomy/gi2taxonomy.xml
@@ -9,6 +9,9 @@
   <outputs>
     <data format="taxonomy" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="binary">taxBuilder</requirement>
+  </requirements>
   <tests>
     <test>
       <param name="input" value="taxonomy2gi-input.txt"/>
diff --git a/tools/taxonomy/t2ps_wrapper.xml b/tools/taxonomy/t2ps_wrapper.xml
index 996df15de73..7e66dbb1f42 100644
--- a/tools/taxonomy/t2ps_wrapper.xml
+++ b/tools/taxonomy/t2ps_wrapper.xml
@@ -37,6 +37,9 @@
   <outputs>
     <data format="pdf" name="out_file1" />
   </outputs>
+  <requirements>
+    <requirement type="binary">tree2PS-fast</requirement>
+  </requirements>
   <help>
 
 **What it does**
diff --git a/tools/taxonomy/t2t_report.xml b/tools/taxonomy/t2t_report.xml
index 16f6c42755d..8d541f18d69 100644
--- a/tools/taxonomy/t2t_report.xml
+++ b/tools/taxonomy/t2t_report.xml
@@ -7,7 +7,10 @@
     <outputs>
         <data format="tabular" name="out_file1" />
     </outputs>
-      <tests>
+  <requirements>
+    <requirement type="binary">taxonomy2tree</requirement>
+  </requirements>
+  <tests>
     <test>
       <param name="input" value="taxonomyGI.dat" ftype="taxonomy"/>
       <output name="out_file1" file="t2t_report.dat"/>