# HG changeset patch
# User yhoogstrate
# Date 1464074863 14400
# Node ID 3fbde4864e00fb334c93ce141f6e724556e65d93
# Parent  b7c313dbaa4bc0e0431b59cbed98e01cd62b7005
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3814f709ce964e99fe3cf2f979c11f8f3b87bce3-dirty

diff -r b7c313dbaa4b -r 3fbde4864e00 macros.xml
--- a/macros.xml	Sun May 22 13:20:01 2016 -0400
+++ b/macros.xml	Tue May 24 03:27:43 2016 -0400
@@ -16,6 +16,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     ]]></token>
 
diff -r b7c313dbaa4b -r 3fbde4864e00 test-data/.directory
--- a/test-data/.directory	Sun May 22 13:20:01 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-[Dolphin]
-Timestamp=2016,4,26,17,37,35
-Version=3
-ViewMode=2
diff -r b7c313dbaa4b -r 3fbde4864e00 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun May 22 13:20:01 2016 -0400
+++ b/tool_dependencies.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="segmentation-fold" version="1.6.5">
-        <repository changeset_revision="3861f2be5d38" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d4e473560ae5" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
 
@@ -14,8 +14,11 @@
     <package name="pysam" version="0.8.2.1">
         <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="htseq" version="0.6.1">
+        <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     
     <package name="segmentation-fold-utils" version="2.0.0">
-        <repository changeset_revision="3861f2be5d38" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d4e473560ae5" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_add-read-counts.xml
--- a/utils_add-read-counts.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_add-read-counts.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_add-read-counts" name="add-read-counts" version="@VERSION@-0">
+<tool id="smf_utils_add-read-counts" name="add-read-counts" version="@VERSION@-3">
     <description>Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     </requirements>
     <expand macro="stdio" />
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_estimate-energy.xml
--- a/utils_estimate-energy.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_estimate-energy.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-1">
+<tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-2">
     <description>Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
 
         <requirement type="package" version="1.6.5">segmentation-fold</requirement>
@@ -71,7 +72,7 @@
                value="0"
                min="0"
                argument="--randomize"
-               label="Shuffle each sequence this many times and predict energy of shuffled sequence(s) (default: 0, 0 means disabled)" />
+               label="Shuffle each sequence this many times and predict energy of shuffled sequence(s)·(default:·0,·0·means·disabled)" />
         
         <param name="sequences_from_fasta_file"
                type="data"
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_extract-boxed-sequences.xml
--- a/utils_extract-boxed-sequences.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_extract-boxed-sequences.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_extract-boxed-sequences" name="extract-boxed-sequences" version="@VERSION@-0">
+<tool id="smf_utils_extract-boxed-sequences" name="extract-boxed-sequences" version="@VERSION@-1">
     <description>Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     </requirements>
     <expand macro="stdio" />
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_filter-annotated-entries.xml
--- a/utils_filter-annotated-entries.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_filter-annotated-entries.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_filter-annotated-entries" name="filter-annotated-entries" version="@VERSION@-0">
+<tool id="smf_utils_filter-annotated-entries" name="filter-annotated-entries" version="@VERSION@-1">
     <description>Split entries into two files based on whether they overlap annotations in a bed file</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     </requirements>
     <expand macro="stdio" />
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_filter-by-energy.xml
--- a/utils_filter-by-energy.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_filter-by-energy.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-0">
+<tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-1">
     <description>Split entries over two files based on the estimated energy</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     </requirements>
     <expand macro="stdio" />
diff -r b7c313dbaa4b -r 3fbde4864e00 utils_find-boxes.xml
--- a/utils_find-boxes.xml	Sun May 22 13:20:01 2016 -0400
+++ b/utils_find-boxes.xml	Tue May 24 03:27:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="smf_utils_find-boxes" name="find-boxes" version="@VERSION@-0">
+<tool id="smf_utils_find-boxes" name="find-boxes" version="@VERSION@-1">
     <description>Finds all occurances of two given boxes (sequence motifs) within a FASTA file</description>
     
     <macros>
@@ -9,6 +9,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
     </requirements>