| Previous changeset 0:8f24f22f9e59 (2016-06-24) Next changeset 2:53b704cc17ad (2017-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9 |
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modified:
README chimera.pintail.xml macros.xml test-data/98_sq_phylip_amazon.dist test-data/Fasting_Example1.fasta test-data/Fasting_Example1.qual test-data/Fasting_Example1.sff test-data/Fasting_Example2.sff test-data/GQY1XT001.oligos test-data/HMP_MOCK.v35.align test-data/HMP_MOCK.v35.align.names test-data/HMP_MOCK.v35.fasta test-data/HMP_MOCK.v35.pintail.quan test-data/HMP_MOCK.v35.slayer.chimeras test-data/HMPv5-v3_1368-1369.oligos test-data/LookUp_Titanium.pat test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg test-data/Mock_S280_L001_R1_001_small.contigs.report test-data/Mock_S280_L001_R1_001_small.fastq test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary test-data/Mock_S280_L001_R2_001_small.fastq test-data/abrecovery.groups test-data/abrecovery.names test-data/abrecovery.pds.wang.taxonomy test-data/abrecovery.pds.wang.tree.sum test-data/abrecovery.tre test-data/amazon.accnos.otulabels test-data/amazon.align_head test-data/amazon.align_head.count_table test-data/amazon.align_head.list test-data/amazon.align_head.names test-data/amazon.align_head.wang.taxonomy test-data/amazon.align_head_short test-data/amazon.an.0.03.-.0.05.otu.hierarchy test-data/amazon.an.jclass.unique.tre test-data/amazon.an.list test-data/amazon.an.rabund test-data/amazon.an.rabund2 test-data/amazon.an.relabund test-data/amazon.an.sabund test-data/amazon.an.sabund2 test-data/amazon.an.sabund3 test-data/amazon.an.shared test-data/amazon.bad.accnos test-data/amazon.count_table test-data/amazon.design test-data/amazon.dist test-data/amazon.fasta test-data/amazon.fasta_head test-data/amazon.fragclust.fasta test-data/amazon.fragclust.names test-data/amazon.groupaccnos test-data/amazon.groups test-data/amazon.head.names test-data/amazon.metadata test-data/amazon.mothur.shared test-data/amazon.names test-data/amazon.pair.dist test-data/amazon.pcoa.axes test-data/amazon.pcoa.loadings test-data/amazon.silva.wang.tax.summary test-data/amazon.square.pcoa.axes test-data/amazon.unique.fasta test-data/amazon.unique.names test-data/amazon.wang.knn.tax.summary test-data/amazon.wang.wang.taxonomy test-data/amazon1.count_table test-data/amazon1.names test-data/amazon_withgroups.count_table test-data/amazon_withgroups.redundant.groups test-data/amazon_withgroups_pasture.count_table test-data/biosample.source test-data/biosample.tsv test-data/biosample.xml test-data/cd-test.constaxonomy test-data/cd-test.database test-data/cd-test.list test-data/cd-test.repfasta test-data/cd-test.repname test-data/env.dist test-data/example.biom test-data/example.constaxonomy test-data/final.tx.1.cons.taxonomy test-data/final.tx.1.subsample.1.pick.shared test-data/makesra.project test-data/metadata test-data/mock.flow test-data/output.fa test-data/sample1.fa test-data/sample2.fa test-data/sample3.fa test-data/silva.ss.map.head test-data/testflow.flow test-data/toymothur.design test-data/toymothur.design2 test-data/treetest.deunique.tre test-data/treetest.groups test-data/treetest.names test-data/treetest.tre test-data/veg.dist tool-data/mothur_aligndb.loc.sample tool-data/mothur_lookup.loc.sample tool-data/mothur_map.loc.sample tool-data/mothur_taxonomy.loc.sample tool_data_table_conf.xml.sample |
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added:
test-data/cd-test.count_table test-data/mouse.design tools.yaml |
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removed:
tool_dependencies.xml |
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| diff -r 8f24f22f9e59 -r b281cc5f8e01 README --- a/README Fri Jun 24 17:34:24 2016 -0400 +++ b/README Thu May 18 18:25:55 2017 -0400 |
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| @@ -4,8 +4,11 @@ - Provides Mothur wrappers for the Mothur tools - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system -Requirements: - - Build utilities (make, GCC, gfortran, etc) +Installing Tools via the API: +This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead + - Install ephemeris: pip install ephemeris -U + - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml + - (You can find a tools.yaml you can use in this repo as well) Installing reference data from silva and greengenes: - There is a Galaxy datamanager for available for Mothur |
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| diff -r 8f24f22f9e59 -r b281cc5f8e01 chimera.pintail.xml --- a/chimera.pintail.xml Fri Jun 24 17:34:24 2016 -0400 +++ b/chimera.pintail.xml Thu May 18 18:25:55 2017 -0400 |
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| @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$fasta" fasta.dat && ln -s "$alignment.template" alignment.template.dat && @@ -40,6 +43,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> @@ -119,15 +123,12 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The chimera.pintail_ command identifies putative chimeras using the pintail approach. It looks at the variation between the expected differences and the observed differences in the query sequence over several windows. This method was written using the algorithms described in the paper_ "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1. - -From www.bioinformatics-toolkit.org_ - The Pintail algorithm is a technique for determining whether a 16S rDNA sequence is anomalous. It is based on the idea that the extent of local base differences between two aligned 16S rDNA sequences should be roughly the same along the length of the alignment (having allowed for the underlying pattern of hypervariable and conserved regions known to exist within the 16S rRNA gene). In other words, evolutionary distance between two reliable sequences should be constant along the length of the gene. In contrast, if an error-free sequence is compared with an anomalous sequence, evolutionary distance along the alignment is unlikely to be constant, especially if the anomaly in question is a chimera and formed from phylogenetically different parental sequences. @@ -140,10 +141,11 @@ .. _paper: http://www.ncbi.nlm.nih.gov/pubmed/16332745 -.. _www.bioinformatics-toolkit.org: http://www.bioinformatics-toolkit.org/Help/Topics/pintailAlgorithm.html -.. _chimera.pintail: http://www.mothur.org/wiki/Chimera.pintail +.. _chimera.pintail: https://www.mothur.org/wiki/Chimera.pintail ]]> </help> - <expand macro="citations"/> + <expand macro="citations"> + <citation type="doi">10.1128/AEM.71.12.7724-7736.2005</citation> + </expand> </tool> |
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| diff -r 8f24f22f9e59 -r b281cc5f8e01 macros.xml --- a/macros.xml Fri Jun 24 17:34:24 2016 -0400 +++ b/macros.xml Thu May 18 18:25:55 2017 -0400 |
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| @@ -7,7 +7,14 @@ <xml name="version_command"> <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> </xml> + <xml name="stdio"> + <stdio> + <regex match="\[ERROR\]" source="stdout" level="fatal"/> + <exit_code range="1:" level="fatal"/> + </stdio> + </xml> <token name="@WRAPPER_VERSION@">1.36.1</token> + <token name="@SHELL_OPTIONS@">set -o pipefail;</token> <token name="@MOTHUR_OVERVIEW@"> <![CDATA[ @@ -16,7 +23,7 @@ Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. -.. _Mothur-Wiki: http://www.mothur.org/wiki/Main_Page +.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page ]]> </token> @@ -25,8 +32,54 @@ <filter type="data_meta" ref="otu" key="labels"/> </options> </xml> + <xml name="calc-common"> + <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first --> + <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="canberra">canberra - Community Structure Similarity</option> + <option value="gower">gower - Community Structure Similarity</option> + <option value="hamming">hamming - Community Membership Similarity</option> + <option value="hellinger">hellinger - Community Structure Similarity</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="jsd">jsd</option> + <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> + <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> + <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> + <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> + <option value="manhattan">manhattan - Community Structure Similarity</option> + <option value="memchi2">memchi2 - Community Membership Similarity</option> + <option value="memchord">memchord - Community Membership Similarity</option> + <option value="memeuclidean">memeuclidean - Community Membership Similarity</option> + <option value="mempearson">mempearson - Community Membership Similarity</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> + <option value="odum">odum - Community Structure Similarity</option> + <option value="rjsd">rjsd</option> + <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> + <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> + <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> + <option value="soergel">soergel - Community Structure Similarity</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="spearman">spearman - Community Structure Similarity</option> + <option value="speciesprofile">speciesprofile - Community Structure Similarity</option> + <option value="structchi2">structchi2 - Community Structure Similarity</option> + <option value="structchord">structchord - Community Structure Similarity</option> + <option value="structeuclidean">structeuclidean - Community Structure Similarity</option> + <option value="structkulczynski">structkulczynski - Community Structure Similarity</option> + <option value="structpearson">structpearson - Community Structure Similarity</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> + <yield/> + </xml> <xml name="logfile-output"> - <data name="logfile" format="txt" from_work_dir="mothur.*.logfile" label="${tool.name} on ${on_string}: logfile"/> + <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> </xml> <xml name="logfile-test"> <output name="logfile" ftype="txt"> |
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| diff -r 8f24f22f9e59 -r b281cc5f8e01 test-data/cd-test.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.count_table Thu May 18 18:25:55 2017 -0400 |
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| @@ -0,0 +1,6 @@ +Representative_Sequence total +GQY1XT001C296C 4 +GQY1XT001AUA36 1 +GQY1XT001DLSKT 1 +GQY1XT001B3W8S 1 +GQY1XT001A4UXI 1 |
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| diff -r 8f24f22f9e59 -r b281cc5f8e01 test-data/mock.flow --- a/test-data/mock.flow Fri Jun 24 17:34:24 2016 -0400 +++ b/test-data/mock.flow Thu May 18 18:25:55 2017 -0400 |
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| b'@@ -1,10 +1,108 @@\n 450\n-GQY1XT001ARI8V 450 1.08 0.00 1.01 0.00 0.00 0.96 0.00 1.05 0.00 2.20 2.19 1.04 1.05 0.00 0.00 1.02 1.04 0.00 2.99 0.94 0.94 0.00 1.06 0.07 0.05 1.96 0.04 0.00 1.86 0.15 0.89 0.00 0.14 1.11 0.04 0.00 2.67 0.05 0.00 0.98 0.21 0.95 0.00 1.13 2.79 0.11 0.96 0.08 0.21 1.96 2.05 0.00 1.93 0.15 0.13 0.82 0.14 0.00 0.94 1.95 0.99 0.00 1.08 1.20 1.06 1.08 0.97 0.09 1.10 0.08 4.02 0.00 0.06 1.00 0.34 1.75 0.00 0.08 0.91 2.15 0.00 0.93 0.10 1.13 0.93 0.10 0.00 1.02 0.11 0.02 0.92 0.12 1.86 2.05 0.11 0.00 1.20 0.20 0.00 0.91 0.10 0.01 0.91 1.11 1.86 1.03 0.10 1.08 0.17 0.09 0.92 0.14 0.96 0.00 0.10 1.01 0.13 0.00 1.06 0.10 0.00 0.93 0.08 1.01 0.00 0.07 1.00 0.10 0.00 1.06 1.10 0.12 1.03 2.21 0.13 3.51 0.06 0.18 1.00 2.23 0.04 2.70 4.49 0.20 0.94 2.03 1.49 0.02 0.13 1.14 1.07 0.02 1.78 1.03 0.16 0.87 0.20 0.13 0.87 0.12 0.06 0.97 1.12 0.01 0.97 0.13 1.09 0.00 0.08 1.03 0.13 0.02 0.99 0.09 1.02 0.94 2.94 1.17 1.12 1.95 0.31 0.07 1.03 1.16 1.00 0.01 0.13 2.00 0.13 0.91 0.87 0.22 0.95 1.04 2.00 0.13 0.13 1.10 0.14 2.82 0.85 1.03 0.04 0.33 0.99 0.06 0.97 0.06 1.09 1.91 0.11 0.00 1.04 0.22 1.97 0.04 1.07 0.03 0.14 1.04 2.80 0.00 0.01 1.12 0.40 0.92 0.01 0.09 0.97 0.10 3.62 0.08 0.13 0.87 1.42 0.93 0.03 0.07 1.00 0.09 2.91 0.01 1.11 0.97 0.37 0.00 1.09 0.12 0.00 1.00 1.07 0.03 0.07 1.08 0.15 0.01 1.09 0.11 1.02 0.05 0.04 0.88 0.17 1.04 0.11 0.05 1.08 1.00 1.00 0.11 1.05 0.07 0.12 0.91 0.12 1.03 2.00 1.09 1.08 0.13 0.08 0.85 0.13 0.92 0.08 1.03 1.98 0.09 0.02 1.03 0.12 0.98 0.05 2.82 0.06 0.95 1.13 0.17 1.04 1.10 0.01 0.00 2.07 0.05 2.00 0.03 0.95 0.98 0.09 0.05 1.88 0.05 0.09 1.13 1.13 0.12 1.05 0.00 0.04 2.06 0.95 0.02 0.00 0.99 1.86 0.01 2.02 0.04 1.03 0.03 1.95 0.05 0.04 1.09 0.06 0.01 0.95 0.97 0.08 0.01 1.04 0.02 1.04 0.04 1.00 0.03 1.04 0.08 1.02 0.00 0.08 0.96 0.09 0.01 1.01 1.22 0.09 0.05 1.09 0.04 0.00 1.10 0.06 0.05 3.04 0.10 1.09 0.07 0.15 1.06 1.94 0.95 0.06 0.04 1.05 0.06 1.10 0.94 0.91 0.08 0.03 0.85 0.99 0.03 0.13 0.97 0.06 0.08 1.19 0.01 0.12 1.96 0.11 1.77 0.05 0.00 1.98 0.07 2.08 0.08 0.18 0.90 1.11 0.02 2.97 0.03 1.99 0.03 0.78 0.09 0.84 0.02 1.70 0.05 1.28 0.06 1.25 0.01 0.07 1.13 0.06 0.07 1.02 0.06 0.05 1.10 0.79 0.05 1.12 0.00 1.15 0.09 0.19 1.79 0.09 1.08 4.12 0.12 2.06 0.11 0.17 0.80 0.06 0.77 2.69 0.00 1.99 0.10 0.23 1.65 \n-GQY1XT001AUUKF 450 1.03 0.00 1.05 0.00 0.00 0.96 0.00 1.01 0.00 2.13 2.10 1.10 0.99 0.00 0.00 0.93 1.09 0.00 3.08 1.03 0.98 0.00 0.96 0.00 0.00 2.05 0.00 0.00 1.95 0.02 2.07 0.00 3.00 2.22 0.01 0.98 3.57 0.99 0.01 0.87 0.94 0.10 1.04 0.00 1.96 0.00 0.00 1.04 0.07 0.00 1.03 1.14 0.04 1.03 2.12 1.02 1.05 1.15 1.03 0.00 1.08 0.00 3.81 0.00 0.02 0.90 0.12 1.89 0.00 0.09 0.93 2.06 0.00 1.77 0.09 0.11 0.93 1.11 0.92 0.01 1.80 1.93 0.12 0.00 1.18 0.27 0.00 0.90 0.12 0.00 0.91 1.08 1.84 1.01 0.14 1.10 0.24 0.13 0.90 1.96 0.03 0.00 1.05 2.01 0.02 0.00 0.99 0.16 0.00 1.01 1.13 0.04 0.00 1.05 0.11 1.09 0.02 0.98 0.05 2.05 0.94 0.11 1.00 0.10 0.13 0.84 0.06 0.08 0.98 0.10 0.00 1.09 0.13 1.01 0.96 0.15 0.04 1.99 3.79 0.11 1.02 1.27 1.28 0.00 0.14 0.91 2.16 0.03 0.99 1.08 0.15 0.91 1.00 1.08 0.11 0.12 2.07 0.12 0.97 0.07 0.13 0.99 0.12 0.02 0.92 0.11 1.01 0.99 2.79 1.03 1.09 1.86 0.20 0.07 0.97 1.11 0.95 0.06 0.11 1.98 0.20 1.08 1.01 0.16 0.94 1.02 2.05 0.10 0.10 1.08 0.08 2.87 1.03 0.92 0.04 0.24 1.04 0.09 1.06 0.05 1.06 1.91 0.09 0.00 0.86 0.14 1.94 0.16 1.08 0.04 0.04 1.06 2.89 0.00 0.12 0.95 0.15 0.10 1.03 0.05 1.06 0.05 3.88 0.07 0.12 0.95 1.03 1.08 0.13 0.12 1.03 0.09 2.98 0.04 1.03 0.91 0.12 0.91 0.12 0.96 0.13 0.07 1.99 0.03 1.15 0.04 1.03 0.11 0.06 0.97 0.05 1.08 1.13 0.03 0.11 1.09 1.06 0.08 1.11 0.09 0.13 0.97 0.05 0.96 2.09 0.92 1.03 0.06 0.06 0.95 0.02 1.02 1.05 0.02 1.93 0.05 0.10 0.92 0.11 0.92 0.12 2.95 0.11 1.01 1.24 0.07 0.97 0.99 0.14 0.09 2.02 0.10 2.02 0.07 0.80 1.00 0.03 0.09 2.08 0.04 0.13 1.25 1.01 0.00 0.95 0.08 0.00 2.11 0.95 1.09 0.09 0.02 1.72 0.03 1.22 0.10 1.81 0.11 2.12 0.04 1.03 1.97 0.08 0.05 0.79 0.00 1.09 0.01 0.93 0.10 1.04 0.04 1.08 0.93 0.83 1.29 0.12'..b'5 1.10 0.03 0.02 1.06 0.04 0.97 0.00 0.09 1.04 0.96 0.03 1.02 0.05 0.99 0.01 0.09 0.97 0.09 1.16 0.03 1.02 0.04 0.01 1.01 0.05 1.05 0.03 1.00 0.05 1.02 0.00 0.11 0.93 1.00 0.03 1.12 0.02 1.07 1.00 0.09 1.05 3.10 1.04 0.04 1.91 0.96 0.04 0.08 2.00 0.06 0.05 2.03 1.02 0.04 1.01 1.03 0.98 0.10 0.10 2.01 0.09 1.05 0.05 0.06 1.05 0.10 0.08 1.07 0.06 1.03 1.06 2.93 1.12 1.01 0.05 0.90 0.10 0.10 0.96 0.13 0.00 1.02 1.04 0.98 0.07 0.07 2.02 0.12 0.89 1.13 0.01 0.95 1.03 1.93 0.09 0.08 0.96 0.02 2.97 1.00 1.08 0.09 0.00 1.02 0.11 1.08 0.03 0.94 1.97 0.03 0.03 0.98 0.01 2.09 0.08 1.09 0.08 0.11 1.03 2.01 0.07 1.07 0.96 0.12 0.98 0.10 0.07 1.08 1.11 3.09 0.09 0.04 0.94 1.02 1.07 0.16 0.08 1.07 0.05 2.94 0.05 0.90 1.02 0.85 0.01 0.11 1.02 0.10 0.04 0.96 0.00 2.16 0.06 1.03 0.08 0.04 1.00 0.09 1.03 0.07 0.03 1.09 1.06 1.19 0.06 1.03 0.06 0.11 0.96 0.06 0.99 2.08 0.08 0.12 2.96 0.01 0.05 0.99 0.76 0.08 0.05 2.03 2.02 1.01 0.97 0.02 0.03 1.02 0.00 0.04 1.09 0.05 0.02 1.11 0.10 1.07 0.03 0.00 1.07 0.02 0.00 2.07 0.10 2.08 0.03 0.83 1.07 0.06 0.01 1.06 0.08 0.04 1.97 0.04 0.02 1.15 0.01 1.07 2.00 0.01 0.91 0.07 0.81 2.06 0.00 1.10 0.10 0.88 0.03 0.10 1.09 0.07 0.04 1.07 0.93 1.13 0.09 0.02 1.02 0.10 1.03 0.11 0.02 1.07 0.96 0.06 0.07 1.05 0.06 0.97 0.14 0.84 1.05 0.06 0.03 0.90 0.02 0.04 1.11 0.11 0.03 1.07 0.00 0.11 1.04 0.11 0.07 3.16 0.04 0.99 0.06 0.01 1.05 2.02 1.17 0.08 0.06 0.82 0.00 1.28 1.16 1.05 0.08 0.05 0.74 2.10 0.11 0.13 1.08 0.76 0.98 0.12 0.10 1.14 0.06 0.10 1.06 0.10 0.05 1.99 0.07 2.06 1.04 0.11 0.00 1.02 0.02 0.11 1.04 0.11 0.06 0.99 0.99 1.13 0.13 1.95 0.11 1.06 0.01 1.01 0.13 0.86 0.91 0.19 0.00 2.96 0.06 0.07 1.00 1.01 0.07 1.15 0.00 1.16 0.09 0.06 2.03 0.11 1.02 0.16 0.78 1.10 0.02 0.09 1.87 \n+GQY1XT001AWPWA 450 1.01 0.00 1.03 0.00 0.00 1.01 0.00 1.02 1.03 0.06 0.00 2.13 1.04 0.00 0.00 1.06 0.04 2.10 3.04 1.04 1.01 0.00 1.00 0.00 0.00 2.21 0.00 0.00 2.07 0.00 1.97 0.00 2.78 2.24 0.00 0.89 2.91 0.04 0.98 0.00 0.02 1.10 1.91 1.08 2.11 0.00 0.05 0.93 0.03 0.07 2.05 1.95 0.13 0.00 0.97 0.99 1.05 1.11 0.96 0.05 1.00 0.03 3.80 0.01 0.06 1.03 0.11 2.03 1.06 0.03 0.13 1.92 0.03 1.00 0.10 0.98 0.00 0.00 1.04 1.11 0.03 0.00 0.96 0.11 2.03 2.12 0.94 1.06 0.13 0.06 1.05 0.00 3.15 0.12 0.86 0.89 0.10 0.00 0.93 0.07 0.95 0.00 0.04 1.13 1.13 0.04 0.00 2.00 0.06 0.00 1.06 0.11 0.07 1.00 2.89 0.10 0.00 1.01 0.05 4.05 0.01 0.06 1.95 0.05 0.04 1.15 0.08 0.03 1.95 0.11 5.45 1.82 0.13 1.04 1.06 0.43 0.06 1.01 1.97 0.05 0.91 1.19 0.30 0.88 0.12 0.14 1.02 1.02 0.03 0.00 1.06 0.08 1.01 0.03 1.11 0.00 0.13 1.02 0.12 0.00 1.02 0.13 0.99 1.02 2.89 1.06 1.96 1.05 0.30 0.09 1.15 1.06 0.98 0.06 0.10 1.98 0.16 0.94 0.89 0.17 0.99 1.10 1.90 0.03 0.12 1.02 0.19 2.83 0.92 1.07 0.06 0.24 1.06 0.07 1.05 0.05 1.04 1.90 0.09 0.08 0.97 0.15 1.93 0.05 1.02 0.04 0.18 1.07 1.99 0.13 0.91 1.00 0.13 0.95 0.18 0.06 1.03 0.11 3.39 0.10 0.14 0.85 1.28 1.01 0.02 0.05 0.95 0.07 2.97 0.02 1.07 0.93 1.18 0.00 0.11 1.09 0.10 0.00 1.10 0.03 2.02 0.05 1.01 0.08 0.17 0.86 0.08 0.90 0.13 0.06 1.01 1.09 1.03 0.08 1.03 0.10 0.09 0.93 0.09 0.91 0.95 1.00 0.09 1.90 0.08 1.89 0.11 1.06 0.08 0.05 1.90 1.88 0.05 0.12 1.01 0.11 0.18 0.99 0.10 0.07 0.90 0.01 0.10 1.08 0.09 0.04 1.14 0.07 0.96 0.07 0.00 1.01 0.08 0.07 1.76 0.03 1.89 0.04 0.96 1.06 0.11 0.11 1.08 0.10 0.10 1.93 0.09 0.04 1.02 0.03 1.00 3.69 1.80 0.06 0.98 0.11 1.02 0.05 0.07 0.98 0.10 0.00 0.93 1.12 1.11 0.03 0.11 0.96 0.07 0.93 0.10 0.00 1.08 0.97 0.06 0.04 1.02 0.05 0.92 0.03 1.04 1.08 0.09 0.06 1.06 0.01 0.02 0.99 0.16 0.10 1.09 0.07 0.13 1.08 0.09 0.09 2.85 0.10 1.01 0.05 0.13 0.97 1.89 0.98 0.15 0.06 0.99 0.01 1.04 1.13 1.12 0.02 0.05 0.87 1.79 0.06 0.09 1.10 1.00 1.04 0.18 0.10 0.95 0.06 0.09 1.04 0.06 0.08 2.31 0.03 2.00 1.21 0.04 0.09 0.92 0.00 0.12 0.93 0.10 0.00 0.99 1.13 1.05 0.03 2.09 0.01 1.09 0.02 0.84 0.08 1.06 0.03 2.04 0.09 1.87 0.01 0.17 1.01 1.13 0.03 1.02 0.00 0.94 0.09 0.07 2.12 0.06 1.06 0.08 0.90 0.10 0.09 1.12 0.11 1.07 1.01 0.18 0.08 1.97 0.00 0.27 1.04 0.03 1.08 3.12 0.15 1.06 0.00 0.10 1.85 \n' |
| b |
| diff -r 8f24f22f9e59 -r b281cc5f8e01 test-data/mouse.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse.design Thu May 18 18:25:55 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +group dpw +F003D000 0 +F003D142 142 +F003D144 144 +F003D146 146 +F003D148 148 +F003D150 150 +F003D002 2 +F003D006 6 +F003D008 8 |
| b |
| diff -r 8f24f22f9e59 -r b281cc5f8e01 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Jun 24 17:34:24 2016 -0400 +++ b/tool_data_table_conf.xml.sample Thu May 18 18:25:55 2017 -0400 |
| b |
| @@ -1,17 +1,17 @@ <tables> - <table name="mothur_aligndb" comment_char="#"> + <table name="mothur_aligndb" comment_char="#" allow_duplicate_entries="False"> <columns>name, value</columns> <file path="tool-data/mothur_aligndb.loc" /> </table> - <table name="mothur_lookup" comment_char="#"> + <table name="mothur_lookup" comment_char="#" allow_duplicate_entries="False"> <columns>name, value</columns> <file path="tool-data/mothur_lookup.loc" /> </table> - <table name="mothur_map" comment_char="#"> + <table name="mothur_map" comment_char="#" allow_duplicate_entries="False"> <columns>name, value</columns> <file path="tool-data/mothur_map.loc" /> </table> - <table name="mothur_taxonomy" comment_char="#"> + <table name="mothur_taxonomy" comment_char="#" allow_duplicate_entries="False"> <columns>name, value</columns> <file path="tool-data/mothur_taxonomy.loc" /> </table> |
| b |
| diff -r 8f24f22f9e59 -r b281cc5f8e01 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 24 17:34:24 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="legacy_blast" version="2.2.22"> - <repository changeset_revision="b2a669334165" name="package_legacy_blast_2_2_22" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="boost" version="1.57"> - <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="zlib" version="1.2.8"> - <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="mothur" version="1.36.1"> - <repository changeset_revision="29af213dbe4c" name="package_mothur_1_36_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r 8f24f22f9e59 -r b281cc5f8e01 tools.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools.yaml Thu May 18 18:25:55 2017 -0400 |
| b |
| b'@@ -0,0 +1,802 @@\n+---\n+# This is a sample file to be used as a reference for populating a list of\n+# tools that you wish to install into Galaxy from a Tool Shed via the\n+# `install_tool_shed_tools.py` script.\n+#\n+# For each tool you want to install, you must provide the following keys:\n+# * name: this is is the name of the tool to install\n+# * owner: owner of the Tool Shed repository from where the tools is being\n+# installed\n+# Further, you need to provide **one** of the following two keys:\n+# * tool_panel_section_id: ID of the tool panel section where you want the\n+# tool to be installed. The section ID can be found\n+# in Galaxy\'s `shed_tool_conf.xml` config file. Note\n+# that the specified section must exist in this file.\n+# Otherwise, the tool will be installed outside any\n+# section.\n+# * tool_panel_section_label: Display label of a tool panel section where\n+# you want the tool to be installed. If it does not\n+# exist, this section will be created on the target\n+# Galaxy instance (note that this is different than\n+# when using the ID).\n+# Multi-word labels need to be placed in quotes.\n+# Each label will have a corresponding ID created;\n+# the ID will be an all lowercase version of the\n+# label, with multiple words joined with\n+# underscores (e.g., \'BED tools\' -> \'bed_tools\').\n+#\n+# Tou can also specify the following optional keys to further define the\n+# installation properties:\n+# * tool_shed_url: the URL of the Tool Shed from where the tool should be\n+# installed. (default: https://toolshed.g2.bx.psu.edu)\n+# * revisions: a list of revisions of the tool, all of which will attempt to\n+# be installed. (default: latest)\n+# * install_tool_dependencies: True or False - whether to install tool\n+# dependencies or not. (default: True)\n+# * install_repository_dependencies: True or False - whether to install repo\n+# dependencies or not. (default: True)\n+\n+\n+# pip install ephemeris -U\n+# shed_install -t tools.yaml -a <galaxy admin API key> -g <galaxy instance>\n+# (the latter two can also be configure inside the yaml with following two lines)\n+#api_key: admin\n+#galaxy_instance: http://localhost:8080/\n+\n+tools:\n+- name: mothur_align_check\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_align_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_amova\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_anosim\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_bin_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_bellerophon\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_ccode\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_labe'..b'true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sffinfo\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_flows\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sort_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_abund\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_groups\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sub_sample\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_qual\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_shared\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_single\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_tax\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_tree_shared\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_flows\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_unweighted\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_weighted\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unique_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_venn\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n' |
