# HG changeset patch
# User drosofff
# Date 1435093109 14400
# Node ID 71b072cf5dde1eff5e97a5c15b963d90a9190163
# Parent  e8bdae1a2bdc42d3fbaf4d7f17a5d955d15fbc39
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r e8bdae1a2bdc -r 71b072cf5dde sRbowtie.xml
--- a/sRbowtie.xml	Tue May 26 18:36:09 2015 -0400
+++ b/sRbowtie.xml	Tue Jun 23 16:58:29 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0">
+<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.1">
     <description>for FASTA small reads</description>
     <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <command interpreter="python"> sRbowtie.py --input $input
                                              --input-format $input.extension
@@ -55,12 +55,12 @@
             </when>
         </conditional>
         <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
-            <option select="true" value="tabular">tabular</option>
+            <option selected="true" value="tabular">tabular</option>
             <option value="sam">sam</option>
             <option value="bam">bam</option>
         </param>
         <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
-            <option select="true" value="No">No</option>
+            <option selected="true" value="No">No</option>
             <option value="al">aligned</option>
             <option value="unal">unaligned</option>
             <option value="al_and_unal">both aligned and unaligned</option>
@@ -105,7 +105,7 @@
             <param ftype="fasta" name="input" value="input.fa" />
             <param name="v_mismatches" value="1" />
             <param name="output_format" value="bam" />
-            <output file="output.bam" ftype="bam" lines_diff="4" name="output" />
+            <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
         </test>
         <test>
             <param name="genomeSource" value="history" />
@@ -114,7 +114,7 @@
             <param ftype="fastq" name="input" value="input.fastq" />
             <param name="v_mismatches" value="1" />
             <param name="output_format" value="bam" />
-            <output file="output2.bam" ftype="bam" lines_diff="4" name="output" />
+            <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
         </test>
     </tests>
     <help>
diff -r e8bdae1a2bdc -r 71b072cf5dde tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 26 18:36:09 2015 -0400
+++ b/tool_dependencies.xml	Tue Jun 23 16:58:29 2015 -0400
@@ -3,7 +3,7 @@
   <package name="bowtie" version="0.12.7">
       <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="0.1.18">
-      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+      <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>