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<?xml version="1.0"?>
<toolbox tool_path="/galaxy/main/shed_tools">
<section id="snpeff" name="snpEff" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>snpeff</repository_name>
<repository_owner>pcingola</repository_owner>
<installed_changeset_revision>c052639fa666</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0</id>
<version>1.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml" guid="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>snpeff</repository_name>
<repository_owner>pcingola</repository_owner>
<installed_changeset_revision>c052639fa666</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0</id>
<version>1.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/22c8c4f8d11c/check_snpeff_candidates/checkSnpEffCandidates.xml" guid="toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>check_snpeff_candidates</repository_name>
<repository_owner>gregory-minevich</repository_owner>
<installed_changeset_revision>22c8c4f8d11c</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0</id>
<version>1.0.0</version>
</tool>
</section>
<section id="ngs-rna-tools" name="NGS: RNA-seq" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/4e6f043995ff/cuffdiff/cuffdiff_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>cuffdiff</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>4e6f043995ff</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2</id>
<version>2.2.1.2</version>
</tool>
</section>
</toolbox>
/Users/lorencm/.virtualenvs/galaxy/bin/python /Users/lorencm/projects/galaxy/importTools2Galaxy.py
1 snpEff
OrderedDict([(u'@file', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml'), (u'@guid', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0'), (u'tool_shed', u'toolshed.g2.bx.psu.edu'), (u'repository_name', u'snpeff'), (u'repository_owner', u'pcingola'), (u'installed_changeset_revision', u'c052639fa666'), (u'id', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0'), (u'version', u'1.0')])
OrderedDict([(u'@file', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml'), (u'@guid', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0'), (u'tool_shed', u'toolshed.g2.bx.psu.edu'), (u'repository_name', u'snpeff'), (u'repository_owner', u'pcingola'), (u'installed_changeset_revision', u'c052639fa666'), (u'id', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0'), (u'version', u'1.0')])
OrderedDict([(u'@file', u'toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/22c8c4f8d11c/check_snpeff_candidates/checkSnpEffCandidates.xml'), (u'@guid', u'toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0'), (u'tool_shed', u'toolshed.g2.bx.psu.edu'), (u'repository_name', u'check_snpeff_candidates'), (u'repository_owner', u'gregory-minevich'), (u'installed_changeset_revision', u'22c8c4f8d11c'), (u'id', u'toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0'), (u'version', u'1.0.0')])
1 NGS: RNA-seq
@file
@guid
tool_shed
repository_name
repository_owner
installed_changeset_revision
id
version
import xmltodict
from pprint import pprint
import os
# wget -c https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/c55aa042825fe02ef4a02d958eb811adba8ea45f/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml
if __name__ == '__main__':
with open('tests/shed_tool_conf.xml') as fd:
doc = xmltodict.parse(fd.read())
for section in doc['toolbox']['section']:
tool_section_name = section['@name']
print "1", tool_section_name
for tool in section['tool']:
print tool
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