Mercurial > repos > drosofff > msp_sr_bowtie_parser
changeset 13:634ad185484b draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | mvdbeek |
|---|---|
| date | Sun, 14 Jun 2015 07:16:33 -0400 |
| parents | e64fec3de201 |
| children | 115af29c4f57 |
| files | sRbowtieParser.xml smRtools.py tool_dependencies.xml |
| diffstat | 3 files changed, 11 insertions(+), 12 deletions(-) [+] |
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--- a/sRbowtieParser.xml Sun Jun 14 06:20:34 2015 -0400 +++ b/sRbowtieParser.xml Sun Jun 14 07:16:33 2015 -0400 @@ -1,11 +1,10 @@ -<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> +<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.5"> <description></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> <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="0.14">scipy</requirement> + <requirement type="package" version="0.12.0">scipy</requirement> </requirements> <command interpreter="python"> sRbowtieParser.py
--- a/smRtools.py Sun Jun 14 06:20:34 2015 -0400 +++ b/smRtools.py Sun Jun 14 07:16:33 2015 -0400 @@ -4,7 +4,8 @@ import sys, subprocess from collections import defaultdict from numpy import mean, median, std -from scipy import stats +##Disable scipy import temporarily, as no working scipy on toolshed. +##from scipy import stats def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"): '''This function will return a dictionary containing fasta identifiers as keys and the @@ -273,6 +274,8 @@ def correlation_mapper (self, reference, window_size): '''to map correlation with a sliding window 26-2-2013''' + from scipy import stats + if window_size > self.size: return [] F=open(reference, "r")
--- a/tool_dependencies.xml Sun Jun 14 06:20:34 2015 -0400 +++ b/tool_dependencies.xml Sun Jun 14 07:16:33 2015 -0400 @@ -3,16 +3,13 @@ <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 name="samtools" version="1.2"> + <repository changeset_revision="77e0e0891773" name="package_samtools_1_2" owner="iuc" 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> - <package name="numpy" version="1.9"> - <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="scipy" version="0.14"> - <repository changeset_revision="8494a6718d89" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="scipy" version="0.12.0"> + <repository changeset_revision="774ce332a3d7" name="package_scipy_0_12_with_atlas" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>