# HG changeset patch
# User drosofff
# Date 1435571813 14400
# Node ID f0b4894486153b5ffa06e3b8119a5c4daba027e4
# Parent  afe1e306e2a86ac75c2f39e486f1b7404477c116
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r afe1e306e2a8 -r f0b489448615 size_histogram.xml
--- a/size_histogram.xml	Sun Jun 21 17:42:14 2015 -0400
+++ b/size_histogram.xml	Mon Jun 29 05:56:53 2015 -0400
@@ -2,7 +2,6 @@
   <description>from sRbowtie aligment</description>
   <requirements>
         <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="2.14">biocbasics</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
@@ -61,7 +60,7 @@
            </param>
            <when value="indexed">
 	     <repeat name="series" title="Add alignment files">
-	       <param name="input" type="data" label="Select multiple alignments to parse">
+	       <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
                   <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
                </param>
 	       <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
@@ -70,12 +69,12 @@
            <when value="history">
               <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
 	     <repeat name="series" title="Add alignment files">
-	       <param name="input" type="data" label="Select multiple alignments to parse"/>
+	       <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
 	       <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
 	     </repeat>
 	   </when>
        </conditional>
-                <param name="gff" type="data" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
+                <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
                  <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
 		<param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
                   <option value="no">for each item</option>
diff -r afe1e306e2a8 -r f0b489448615 smRtools.pyc
Binary file smRtools.pyc has changed
diff -r afe1e306e2a8 -r f0b489448615 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jun 21 17:42:14 2015 -0400
+++ b/tool_dependencies.xml	Mon Jun 29 05:56:53 2015 -0400
@@ -3,9 +3,6 @@
   <package name="bowtie" version="0.12.7">
       <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="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
@@ -13,6 +10,6 @@
         <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
-        <repository changeset_revision="cd2113c820f7" name="package_biocbasics" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="565bfe059907" name="package_biocbasics" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>