Mercurial > repos > drosofff > msp_sr_bowtie_parser

changeset 1:f5388910d083 draft

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Uploaded
author mvdbeek
date Sun, 29 Mar 2015 11:27:33 -0400
parents 3a510730e3fc
children 70193ce0540e
files sRbowtieParser.xml tool_dependencies.xml
diffstat 2 files changed, 16 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/sRbowtieParser.xml	Mon Nov 03 10:27:20 2014 -0500
+++ b/sRbowtieParser.xml	Sun Mar 29 11:27:33 2015 -0400
@@ -4,8 +4,9 @@
 	<requirement type="package" version="0.12.7">bowtie</requirement>
         <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.14">scipy</requirement>
  </requirements>
-  <parallelism method="basic"></parallelism>
 <command interpreter="python">
         sRbowtieParser.py 
 	          #if $refGenomeSource.genomeSource == "history":
@@ -73,13 +74,14 @@
 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**
 
   </help>
-  <test>
+  <tests>
+    <test>
       <param name="genomeSource" value="history" />
       <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
-      <param name="input_list" value="matchedSample_1, matchedSample_2" ftype="tabular" />
+      <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" />
       <param name="polarity" value="forward" />
-      <output name="output" ftype="tabular" value="Read_Count_Lists.tab" />
-  </test>
-
+      <output name="output" ftype="tabular" file="Read_Count_Lists.tab" />
+    </test>
+  </tests>
 </tool>
 
--- a/tool_dependencies.xml	Mon Nov 03 10:27:20 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 29 11:27:33 2015 -0400
@@ -1,12 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
       <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
-      <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository changeset_revision="2e3809844979" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>