nturaga

#!/usr/bin/python
"""
Python script for tailing irc logs and mailing notifications.
"""
import os
import smtplib
import pickle
import copy
from optparse import OptionParser

nturaga

<tool id="bumphunter" name="Bumphunter - Methylation analysis">
    <description>Estimate regions for which a genomic profile deviates from its
     baseline value. Originally implemented to detect differentially
     methylated genomic regions between two populations.</description>
     <requirements>
        <requirement type="binary">Rscript</requirement>
        <requirement type="R-module">Bumphunter</requirement>
        <requirement type="package" version="3.1.1">R_3_1_1</requirement>
        <requirement type="package" version="1.6.0">bumphunter</requirement>
        <!--<requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>-->

nturaga

#!/usr/bin/python

#Write tool to compute GC contect here
# usage : python compute_comething.py <FASTA file> <output file>

import re,sys
import string
 
inp = sys.argv[1]
out = sys.argv[2]

nturaga

<tool id="fa_gc_content_1" name="Compute GC content with python tool">
  <description>for each sequence in a file</description>
  <command interpreter="python">compute_something.py $input $output</command>
  <inputs>
    <param format="fasta" name="input" type="data" label="Source file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>

nturaga

"ack.vim       ctrlp.vim       nerdcommenter  sort-python-imports  vim-hackernews  vim-markdown  vim-scmdiff
"autopep8.vim  jellybeans.vim  pep8           syntastic            vim-irblack     vim-repeat    YouCompleteMe


set nocompatible
filetype off

"Pathogen
call pathogen#infect()
call pathogen#helptags()

nturaga

<tool id="pca1" name="Principal Component Analysis" version="1.0.2">
  <description> </description>
  <requirements>
    <requirement type="package" version="1.0.3">rpy</requirement>
    <requirement type="package" version="2.11.0">R</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
  <command interpreter="python">
    pca.py 
      $input1

nturaga

<tool id="krakentest" name="Kraken" version="0.10.3-beta">
    <requirements>
        <requirement type="package" version="0.10.3-beta">kraken</requirement>
    </requirements>
    <description>
        Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.
    </description>
    <version_command>kraken -version</version_command>
    <command>
        kraken --db

nturaga

<tool id="krakentest" name="Kraken" version="0.10.3-beta">
    <requirements>
        <requirement type="package" version="0.10.3-beta">kraken</requirement>
    </requirements>
    <description>
        Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.
    </description>
    <version_command>kraken -version</version_command>
    <command>
        kraken --db

nturaga

#<unique_build_id>	<dbkey>   <display_name>   <file_path>
krakenMiniDB	miniDB	miniKrakeknDB	/Users/nturaga/Documents/Kraken_galaxy/minikraken_db/

nturaga

<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
<tables>
    <!-- Locations of all fasta files under genome directory -->
    <table name="all_fasta" comment_char="#">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/all_fasta.loc" />
    </table>
    <!-- Locations of indexes in the BFAST mapper format -->
    <table name="bfast_indexes" comment_char="#">
        <columns>value, dbkey, formats, name, path</columns>