| Previous changeset 3:93a451fcde49 (2015-07-07) Next changeset 5:6b468584d645 (2015-09-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit e99d9a3d66e662062cd6d8d601e906c83faef671 |
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modified:
abundance-dist-single.xml abundance-dist.xml count-median.xml do-partition.xml extract-partitions.xml filter-abund.xml filter-below-abund.py filter-below-abund.xml normalize-by-median.xml tool_dependencies.xml |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 abundance-dist-single.xml --- a/abundance-dist-single.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/abundance-dist-single.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-abundance-dist-single" name="Abundance Distribution (all-in-one)" - version="2.0rc1-1"> + version="2.0-1"> <description> Calculate abundance distribution of the k-mers in a given |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 abundance-dist.xml --- a/abundance-dist.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/abundance-dist.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-abundance-dist" name="Abundance Distribution" - version="2.0rc1-1"> + version="2.0-1"> <description> Calculate abundance distribution of the k-mers in a given sequence |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 count-median.xml --- a/count-median.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/count-median.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-count-median" name="Count Median" - version="2.0rc1-1"> + version="2.0-1"> <description> Count the median/avg k-mer abundance for each sequence in the |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 do-partition.xml --- a/do-partition.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/do-partition.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-do-partition" name="Sequence partition all-in-one" - version="2.0rc1-1"> + version="2.0-1"> <description> Load, partition, and annotate FAST[AQ] sequences |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 extract-partitions.xml --- a/extract-partitions.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/extract-partitions.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-extract-partitions" name="Extract partitions" - version="2.0rc1-1"> + version="2.0-1"> <description> Separate sequences that are annotated with partitions into |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 filter-abund.xml --- a/filter-abund.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/filter-abund.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-filter-abund" name="Filter by abundance" - version="2.0rc1-1"> + version="2.0-1"> <description> Trims fastq/fasta sequences at k-mers of a given abundance @@ -46,6 +46,7 @@ <expand macro="input_counting_table_filename" /> </inputs> <outputs> + <!-- <expand macro="output_sequences" /> --> <expand macro="output_sequences_single" /> </outputs> <tests> @@ -54,9 +55,11 @@ <param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" /> <output name="output"> + <!-- <discover_dataset name="test-abund-read-2.fa.abundfilt"> --> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> + <!-- </discover_dataset> --> </output> </test> <test> @@ -66,9 +69,11 @@ value="test-abund-read-2.ct" ftype="ct" /> <param name="cutoff" value="1" /> <output name="output"> + <!-- <discover_dataset name="test-abund-read-2.fa.abundfilt"> --> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> + <!-- </discover_dataset> --> </output> </test> </tests> |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 filter-below-abund.py --- a/filter-below-abund.py Tue Jul 07 13:05:17 2015 -0400 +++ b/filter-below-abund.py Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,10 +1,38 @@ #! /usr/bin/env python -# # This file is part of khmer, https://github.com/dib-lab/khmer/, and is -# Copyright (C) Michigan State University, 2009-2015. It is licensed under -# the three-clause BSD license; see LICENSE. +# Copyright (C) 2011-2015, Michigan State University. +# Copyright (C) 2015, The Regents of the University of California. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# * Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# * Redistributions in binary form must reproduce the above +# copyright notice, this list of conditions and the following +# disclaimer in the documentation and/or other materials provided +# with the distribution. +# +# * Neither the name of the Michigan State University nor the names +# of its contributors may be used to endorse or promote products +# derived from this software without specific prior written +# permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# # Contact: khmer-project@idyll.org -# from __future__ import print_function import sys import os @@ -29,7 +57,7 @@ print('--') print('making hashtable') - ht = khmer.load_counting_hash(counting_ht) + ht = khmer.load_countgraph(counting_ht) K = ht.ksize() for infile in infiles: |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 filter-below-abund.xml --- a/filter-below-abund.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/filter-below-abund.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-filter-below-abund" name="Filter below abundance cutoff of 50" - version="2.0rc1-1"> + version="2.0-1"> <!-- Work in progress, gating on filter-below-abund.py being upgraded --> <description> |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 normalize-by-median.xml --- a/normalize-by-median.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/normalize-by-median.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-normalize-by-median" name="Normalize By Median" - version="2.0rc1-1"> + version="2.0-1"> <description> Filters a fastq/fasta file using digital normalization via |
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| diff -r 93a451fcde49 -r 46f9ee5d0876 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 07 13:05:17 2015 -0400 +++ b/tool_dependencies.xml Wed Sep 09 17:59:01 2015 -0400 |
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| @@ -1,13 +1,13 @@ <?xml version="1.0"?> <tool_dependency> - <package name="khmer" version="2.0rc1"> + <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> - <repository changeset_revision="44bb4258922f" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python" version="2.7" /> </repository> - <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0rc1.tar.gz#md5=d8ea5e3ba34de0380007c74d61fc6d1a</package> + <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610abd021254e21b082179a100cd39</package> </action> </actions> </install> |