--- a/galaxy_integration.org	Fri Dec 08 09:57:17 2017 -0500
+++ b/galaxy_integration.org	Tue Dec 12 04:33:04 2017 -0500
@@ -1,4 +1,5 @@
 #+TITLE: Building galaxy tools
+* Long reads sampling
 #+BEGIN_SRC sh
 # require planemo
 if [ -e "long_reads_sampling.xml" ]
@@ -19,16 +20,42 @@
 | backing         | up      | original | file                         |
 | Tool | written | to       | long_reads_sampling.xml |
 
+
+
+
+* Short read simulator
+#+BEGIN_SRC sh
+# require planemo
+if [ -e "long2short.xml" ]
+then
+   echo "backing up original file"
+   cp long2short.xml long2short.xml.backup
+fi
+/home/petr/anaconda3/bin/planemo tool_init --force  --id 'long2short' \
+--name 'Get pseudo short paired end reads from long reads' \
+--requirement biopython \
+--requirement python@3.6 \
+--example_command 'long2short.py -i input_seq.fasta -o output_seq.fasta -cov coverage -L insert_length -l read_length' \
+--example_input 'input_seq.fasta' \
+--example_output 'output_seq.fasta'
+
+#+END_SRC
+
+#+RESULTS:
+: Tool written to long2short.xml
+
 file must be manually edited
 
+
+* create planemo repo with all tools
 # create toolshed configuration
 #+BEGIN_SRC bash
-planemo shed_init --name=long_reads_sampling \
+/home/petr/anaconda3/bin/planemo shed_init --name=long_reads_sampling \
                     --owner=repeatexplorer \
                     --description=long_reads_sampling \
                     --long_description="Create sample of long reads" \
                     --category="Fasta Manipulation"
-planemo shed_lint --tools
+/home/petr/anaconda3/bin/planemo shed_lint --tools
 #+END_SRC
 
 #+RESULTS: