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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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added:
sc3-kmeans.xml sc3-macros.xml test-data/barcodes.tsv test-data/genes.tsv test-data/pbmc3k.rds test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz test-data/pbmc3k_sc3.rds test-data/scater_log.rds test-data/test |
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| diff -r 000000000000 -r b3c3cf813a49 sc3-kmeans.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sc3-kmeans.xml Wed Apr 03 11:27:08 2019 -0400 |
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| @@ -0,0 +1,63 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="sc3_kmeans" name="SC3 K-Means" version="@TOOL_VERSION@+galaxy0"> + <description>perform k-means clustering</description> + <macros> + <import>sc3-macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +sc3-sc3-kmeans.R -i '${sc3_transformed}' +#if $choose.method == "file": + -k '${choose.sc3_estimated_k}' +#else + -k '${choose.input_k}' +#end if + -o '${sc3_kmeans}' +]]></command> + + <inputs> + <param name="sc3_transformed" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with transformed distances"/> + + <conditional name="choose"> + <param name="method" type="select" label="Method to supply K"> + <option value="input">Enter K as an integer</option> + <option value="file">Provide a text file containing K</option> + </param> + <when value="input"> + <param name="input_k" type="integer" value="0" label="Integer K as the number of clusters for kmeans"/> + </when> + <when value="file"> + <param name="sc3_estimated_k" type="data" format="txt" label="Text file containing estimated K"/> + </when> + </conditional> + </inputs> + + <outputs> + <data name="sc3_kmeans" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object storing the k-means clusters"/> + </outputs> + + <tests> + <test> + <param name="sc3_transformed" value="sc3_transformed.rds"/> + <param name="sc3_estimated_k" value="K_size"/> + <output name="sc3_kmeans" file="sc3_kmeans.rds"/> + </test> + </tests> + + <help><![CDATA[ +========================================= +This function performs kmeans clustering. +========================================= + +It uses transformed distance matrix contained in the transformations item of the +sc3 slot of the metadata(object). It then creates and populates the following +items of the sc3 slot: + +- kmeans: contains a list of kmeans clusterings. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r b3c3cf813a49 sc3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sc3-macros.xml Wed Apr 03 11:27:08 2019 -0400 |
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| @@ -0,0 +1,31 @@ +<macros> + <token name="@TOOL_VERSION@">1.8.0</token> + <token name="@HELP@">Documentation can be found at http://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/SC3.html</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.4">sc3-scripts</requirement> + <yield/> + </requirements> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.8.0+galaxy0: Initial contribution. Ni Huang and Carlos Talavera-Lopez, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.4236</citation> + <citation type="bibtex"> + @misc{githubbioconductor-sc3-scripts.git, + author = {Jonathan Manning, Ni Huang, Jean Chang, Carlos Talavera-López, EBI Gene Expression Team}, + year = {2018}, + title = {SC3-scripts: command line interface for SC3}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts.git}, + }</citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r b3c3cf813a49 test-data/barcodes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes.tsv Wed Apr 03 11:27:08 2019 -0400 |
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| b'@@ -0,0 +1,2700 @@\n+AAACATACAACCAC-1\n+AAACATTGAGCTAC-1\n+AAACATTGATCAGC-1\n+AAACCGTGCTTCCG-1\n+AAACCGTGTATGCG-1\n+AAACGCACTGGTAC-1\n+AAACGCTGACCAGT-1\n+AAACGCTGGTTCTT-1\n+AAACGCTGTAGCCA-1\n+AAACGCTGTTTCTG-1\n+AAACTTGAAAAACG-1\n+AAACTTGATCCAGA-1\n+AAAGAGACGAGATA-1\n+AAAGAGACGCGAGA-1\n+AAAGAGACGGACTT-1\n+AAAGAGACGGCATT-1\n+AAAGATCTGGGCAA-1\n+AAAGCAGAAGCCAT-1\n+AAAGCAGATATCGG-1\n+AAAGCCTGTATGCG-1\n+AAAGGCCTGTCTAG-1\n+AAAGTTTGATCACG-1\n+AAAGTTTGGGGTGA-1\n+AAAGTTTGTAGAGA-1\n+AAAGTTTGTAGCGT-1\n+AAATCAACAATGCC-1\n+AAATCAACACCAGT-1\n+AAATCAACCAGGAG-1\n+AAATCAACCCTATT-1\n+AAATCAACGGAAGC-1\n+AAATCAACTCGCAA-1\n+AAATCATGACCACA-1\n+AAATCCCTCCACAA-1\n+AAATCCCTGCTATG-1\n+AAATGTTGAACGAA-1\n+AAATGTTGCCACAA-1\n+AAATGTTGTGGCAT-1\n+AAATTCGAAGGTTC-1\n+AAATTCGAATCACG-1\n+AAATTCGAGCTGAT-1\n+AAATTCGAGGAGTG-1\n+AAATTCGATTCTCA-1\n+AAATTGACACGACT-1\n+AAATTGACTCGCTC-1\n+AACAAACTCATTTC-1\n+AACAAACTTTCGTT-1\n+AACAATACGACGAG-1\n+AACACGTGCAGAGG-1\n+AACACGTGGAAAGT-1\n+AACACGTGGAACCT-1\n+AACACGTGGCTACA-1\n+AACACGTGTACGAC-1\n+AACAGCACAAGAGT-1\n+AACATTGATGGGAG-1\n+AACCAGTGATACCG-1\n+AACCCAGATCGCTC-1\n+AACCGATGCTCCCA-1\n+AACCGATGGTCATG-1\n+AACCGATGTTCTAC-1\n+AACCGCCTAGCGTT-1\n+AACCGCCTCTACGA-1\n+AACCTACTGTGAGG-1\n+AACCTACTGTGTTG-1\n+AACCTTACGAGACG-1\n+AACCTTACGCGAGA-1\n+AACCTTACTAACGC-1\n+AACCTTTGGACGGA-1\n+AACCTTTGTACGCA-1\n+AACGCAACAAGTAG-1\n+AACGCATGACCCAA-1\n+AACGCATGCCTTCG-1\n+AACGCATGTACTTC-1\n+AACGCCCTCGGGAA-1\n+AACGCCCTCGTACA-1\n+AACGCCCTGCTTAG-1\n+AACGCCCTGGCATT-1\n+AACGTCGAGTATCG-1\n+AACGTGTGAAAGCA-1\n+AACGTGTGGCGGAA-1\n+AACGTGTGTCCAAG-1\n+AACGTGTGTGCTTT-1\n+AACTACCTTAGAGA-1\n+AACTCACTCAAGCT-1\n+AACTCACTTGGAGG-1\n+AACTCGGAAAGTGA-1\n+AACTCGGAAGGTCT-1\n+AACTCTTGCAGGAG-1\n+AACTGTCTCCCTTG-1\n+AACTTGCTACGCTA-1\n+AACTTGCTGGGACA-1\n+AAGAACGAGTGTTG-1\n+AAGAAGACGTAGGG-1\n+AAGACAGAAGTCTG-1\n+AAGACAGAGGATCT-1\n+AAGACAGATTACCT-1\n+AAGAGATGGGTAGG-1\n+AAGATGGAAAACAG-1\n+AAGATGGAGAACTC-1\n+AAGATGGAGATAAG-1\n+AAGATTACAACCTG-1\n+AAGATTACAGATCC-1\n+AAGATTACCCGTTC-1\n+AAGATTACCGCCTT-1\n+AAGATTACCTCAAG-1\n+AAGATTACTCCTCG-1\n+AAGCAAGAGCGAGA-1\n+AAGCAAGAGCTTAG-1\n+AAGCAAGAGGTGTT-1\n+AAGCACTGAGCAAA-1\n+AAGCACTGCATACG-1\n+AAGCACTGGTTCTT-1\n+AAGCCAACGTGTTG-1\n+AAGCCATGAACTGC-1\n+AAGCCATGACACGT-1\n+AAGCCATGCGTGAT-1\n+AAGCCATGTCTCGC-1\n+AAGCCTGACATGCA-1\n+AAGCCTGACCGAAT-1\n+AAGCGACTCCTCAC-1\n+AAGCGACTGTGTCA-1\n+AAGCGACTTACAGC-1\n+AAGCGACTTTGACG-1\n+AAGCGTACGTCTTT-1\n+AAGGCTTGCGAACT-1\n+AAGGTCACGGTTAC-1\n+AAGGTCACTGTTTC-1\n+AAGGTCACTTCCCG-1\n+AAGGTCTGACAGTC-1\n+AAGGTCTGCAGATC-1\n+AAGGTCTGGTATGC-1\n+AAGTAACTCTGAAC-1\n+AAGTAACTGAGATA-1\n+AAGTAGGATACAGC-1\n+AAGTATACCGAACT-1\n+AAGTCCGACTTGTT-1\n+AAGTCCGATAGAAG-1\n+AAGTCTCTAGTCGT-1\n+AAGTCTCTCGGAGA-1\n+AAGTGGCTTGGAGG-1\n+AAGTTCCTCATTCT-1\n+AAGTTCCTTCTTAC-1\n+AATAAGCTCGAATC-1\n+AATAAGCTCGTTGA-1\n+AATACCCTGGACGA-1\n+AATACCCTGGCATT-1\n+AATACTGAAAGGGC-1\n+AATACTGAATTGGC-1\n+AATAGGGAACCCTC-1\n+AATAGGGAGAATGA-1\n+AATCAAACTATCGG-1\n+AATCCGGAATGCTG-1\n+AATCCTACCGGTAT-1\n+AATCCTTGACGGGA-1\n+AATCCTTGGTGAGG-1\n+AATCGGTGGAACTC-1\n+AATCGGTGTGCTTT-1\n+AATCTAGAAAAGTG-1\n+AATCTAGAATCGGT-1\n+AATCTCACAGCCTA-1\n+AATCTCACTCTAGG-1\n+AATCTCTGAACAGA-1\n+AATCTCTGCTTTAC-1\n+AATGATACACCAAC-1\n+AATGATACGGTCAT-1\n+AATGCGTGACACCA-1\n+AATGCGTGGACGGA-1\n+AATGCGTGGCTATG-1\n+AATGGAGAATCGTG-1\n+AATGGAGATCCTTA-1\n+AATGGCTGACACCA-1\n+AATGGCTGCGTGAT-1\n+AATGGCTGTAAAGG-1\n+AATGGCTGTACTCT-1\n+AATGGCTGTGAAGA-1\n+AATGTAACGGTGGA-1\n+AATGTAACGTTTGG-1\n+AATGTCCTCTTCTA-1\n+AATGTTGACAGTCA-1\n+AATGTTGAGTTGAC-1\n+AATGTTGATCTACT-1\n+AATTACGAATTCCT-1\n+AATTACGACTTCTA-1\n+AATTACGAGTAGCT-1\n+AATTACGAGTGAGG-1\n+AATTACGATTGGCA-1\n+AATTCCTGCTCAGA-1\n+AATTGATGTCGCAA-1\n+AATTGTGACTTGGA-1\n+ACAAAGGAGGGTGA-1\n+ACAAATTGATTCTC-1\n+ACAAATTGCTCAGA-1\n+ACAAATTGTTGCGA-1\n+ACAACCGAGGGATG-1\n+ACAACCGAGTTACG-1\n+ACAAGAGAAGTCGT-1\n+ACAAGAGACTTATC-1\n+ACAAGAGAGTTGAC-1\n+ACAATCCTAACCGT-1\n+ACAATCCTTAGCGT-1\n+ACAATTGACTGACA-1\n+ACAATTGATGACTG-1\n+ACACAGACACCTGA-1\n+ACACAGACCATACG-1\n+ACACCAGAGGGCAA-1\n+ACACCCTGGTGTTG-1\n+ACACGAACAGTTCG-1\n+ACACGATGACGCAT-1\n+ACACGATGATGTGC-1\n+ACACGATGTCGTAG-1\n+ACACGATGTGGTCA-1\n+ACAGACACGGCATT-1\n+ACAGACACGTTGTG-1\n+ACAGCAACACCTAG-1\n+ACAGCAACCTCAAG-1\n+ACAGGTACCCCACT-1\n+ACAGGTACGCTGTA-1\n+ACAGGTACTGGTGT-1\n+ACAGTCGACCCAAA-1\n+ACAGTCGACCGATA-1\n+ACAGTGACTCACCC-1\n+ACAGTGACTCTATC-1\n+A'..b'-1\n+TGCTATACTGCTGA-1\n+TGCTGAGAGAGCAG-1\n+TGCTGAGATTATCC-1\n+TGGAAAGACTCTCG-1\n+TGGAAAGAGCGATT-1\n+TGGAAAGAGGTCAT-1\n+TGGAAAGATATGGC-1\n+TGGAACACAAACAG-1\n+TGGAACACGCTAAC-1\n+TGGAAGCTCAGATC-1\n+TGGACCCTACACTG-1\n+TGGACCCTCATGGT-1\n+TGGACCCTGGTACT-1\n+TGGACTGAGTATGC-1\n+TGGAGACTATCAGC-1\n+TGGAGACTGAAACA-1\n+TGGAGACTTCAAGC-1\n+TGGAGACTTGACCA-1\n+TGGAGGGACGGAGA-1\n+TGGAGGGAGCTATG-1\n+TGGATCGATAAAGG-1\n+TGGATGTGACCTAG-1\n+TGGATGTGATGTCG-1\n+TGGATGTGTGAAGA-1\n+TGGATTCTCATACG-1\n+TGGCAATGCTTGTT-1\n+TGGCAATGGAGGGT-1\n+TGGCACCTTCACGA-1\n+TGGCACCTTCAGTG-1\n+TGGGTATGAAGAGT-1\n+TGGGTATGCACAAC-1\n+TGGGTATGGTACGT-1\n+TGGGTATGTTTGGG-1\n+TGGTAGACATGCCA-1\n+TGGTAGACCCTCAC-1\n+TGGTAGACCTGATG-1\n+TGGTAGTGCACTGA-1\n+TGGTATCTAAACAG-1\n+TGGTATCTCTTCCG-1\n+TGGTCAGACCCAAA-1\n+TGGTCAGACCGTTC-1\n+TGGTTACTGACGTT-1\n+TGGTTACTGTTCTT-1\n+TGTAACCTAGAGGC-1\n+TGTAACCTTGCCTC-1\n+TGTAATGACACAAC-1\n+TGTAATGAGGTAAA-1\n+TGTACTTGCTCTAT-1\n+TGTAGGTGCGAGAG-1\n+TGTAGGTGCTATGG-1\n+TGTAGGTGCTCTAT-1\n+TGTAGGTGTGCTGA-1\n+TGTAGTCTTCCAGA-1\n+TGTAGTCTTGCACA-1\n+TGTATCTGTTAGGC-1\n+TGTATGCTCATGGT-1\n+TGTATGCTGTAGGG-1\n+TGTATGCTTTCATC-1\n+TGTCAGGAATACCG-1\n+TGTCAGGAGATGAA-1\n+TGTCTAACCCCTTG-1\n+TGTGACGATTCTCA-1\n+TGTGAGACTGTCAG-1\n+TGTGAGACTTGAGC-1\n+TGTGAGTGACCACA-1\n+TGTGAGTGAGTGCT-1\n+TGTGAGTGGAGATA-1\n+TGTGATCTCTCTAT-1\n+TGTGATCTGACACT-1\n+TGTGGATGGCCAAT-1\n+TGTTAAGACAAAGA-1\n+TGTTAAGATAAGGA-1\n+TGTTAAGATTGGCA-1\n+TGTTACACCGCATA-1\n+TGTTACACGACTAC-1\n+TGTTACTGGCTACA-1\n+TGTTACTGTAGTCG-1\n+TTAACCACCGTAAC-1\n+TTAACCACTAAGGA-1\n+TTAACCACTCAGAC-1\n+TTACACACGTGTTG-1\n+TTACACACTCCTAT-1\n+TTACCATGAATCGC-1\n+TTACCATGGTTGAC-1\n+TTACCATGTGTCTT-1\n+TTACCATGTTGTGG-1\n+TTACGACTGAGAGC-1\n+TTACGACTTGACAC-1\n+TTACGTACGTTCAG-1\n+TTACTCGAACGTTG-1\n+TTACTCGAAGAATG-1\n+TTACTCGACGCAAT-1\n+TTACTCGAGGGTGA-1\n+TTACTCGATCTACT-1\n+TTAGAATGTGGTGT-1\n+TTAGAATGTGTAGC-1\n+TTAGACCTCCTACC-1\n+TTAGACCTCCTTTA-1\n+TTAGCTACAACCGT-1\n+TTAGCTACTGTCCC-1\n+TTAGCTACTTTCGT-1\n+TTAGGGACGCGAAG-1\n+TTAGGGTGCTGGAT-1\n+TTAGGGTGTCCTGC-1\n+TTAGGTCTACTTTC-1\n+TTAGTCACCAGTTG-1\n+TTAGTCTGAAAGCA-1\n+TTAGTCTGCCAACA-1\n+TTAGTCTGTGCACA-1\n+TTATCCGACTAGTG-1\n+TTATCCGAGAAAGT-1\n+TTATGAGAGATAAG-1\n+TTATGCACGTCACA-1\n+TTATGGCTTATGGC-1\n+TTATTCCTATGCTG-1\n+TTATTCCTGGACAG-1\n+TTATTCCTGGTACT-1\n+TTATTCCTTCGTGA-1\n+TTCAAAGATAAAGG-1\n+TTCAACACAACAGA-1\n+TTCAACACCCCAAA-1\n+TTCAACACGGACGA-1\n+TTCAAGCTAAGAAC-1\n+TTCAAGCTAGATGA-1\n+TTCAAGCTGTTGAC-1\n+TTCAAGCTTCCAAG-1\n+TTCAAGCTTGATGC-1\n+TTCAAGCTTTCGCC-1\n+TTCACAACCCGTTC-1\n+TTCACAACGTCTGA-1\n+TTCAGACTACCCAA-1\n+TTCAGACTCTCGAA-1\n+TTCAGTACCGACTA-1\n+TTCAGTACTCAAGC-1\n+TTCAGTACTCCTAT-1\n+TTCAGTTGCCAAGT-1\n+TTCAGTTGTCCTTA-1\n+TTCAGTTGTCTAGG-1\n+TTCAGTTGTCTCGC-1\n+TTCATCGAGGTGGA-1\n+TTCATGTGTGGTGT-1\n+TTCATTCTATGTCG-1\n+TTCATTCTTCTCTA-1\n+TTCCAAACCTATGG-1\n+TTCCAAACCTCCCA-1\n+TTCCAAACTCCCAC-1\n+TTCCAAACTTGACG-1\n+TTCCATGACGAGAG-1\n+TTCCATGACTGTCC-1\n+TTCCCACTTGAGGG-1\n+TTCCCACTTGTCTT-1\n+TTCCTAGAAAGTGA-1\n+TTCCTAGACTAGTG-1\n+TTCGAGGACTCTAT-1\n+TTCGAGGAGGGCAA-1\n+TTCGAGGATAGAAG-1\n+TTCGATTGAGCATC-1\n+TTCGGAGAATGCCA-1\n+TTCGGAGATGTGCA-1\n+TTCGTATGAAAAGC-1\n+TTCGTATGGATAGA-1\n+TTCGTATGGTCTGA-1\n+TTCGTATGTCCTTA-1\n+TTCTACGAACGTAC-1\n+TTCTACGAGTTGGT-1\n+TTCTAGTGACACGT-1\n+TTCTAGTGCATGAC-1\n+TTCTAGTGGAGAGC-1\n+TTCTAGTGGTCACA-1\n+TTCTCAGAAGAGAT-1\n+TTCTCAGAAGCATC-1\n+TTCTCAGATGGAGG-1\n+TTCTGATGGAGACG-1\n+TTCTTACTCTGGAT-1\n+TTGAACCTCCTTGC-1\n+TTGAATGAACTACG-1\n+TTGAATGACTTACT-1\n+TTGAATGATCTCAT-1\n+TTGACACTCTGTAG-1\n+TTGACACTGATAAG-1\n+TTGAGGACAGAACA-1\n+TTGAGGACTACGCA-1\n+TTGAGGTGGACGGA-1\n+TTGCATTGAGCTAC-1\n+TTGCATTGCTAAGC-1\n+TTGCATTGTGACTG-1\n+TTGCTAACACCAAC-1\n+TTGCTAACACGCTA-1\n+TTGCTAACCACTCC-1\n+TTGCTATGGTACGT-1\n+TTGCTATGGTAGGG-1\n+TTGGAGACCAATCG-1\n+TTGGAGACGCTATG-1\n+TTGGAGACTATGGC-1\n+TTGGGAACTGAACC-1\n+TTGGTACTACTGGT-1\n+TTGGTACTCTTAGG-1\n+TTGGTACTGAATCC-1\n+TTGGTACTGGATTC-1\n+TTGTACACGTTGTG-1\n+TTGTACACTTGCAG-1\n+TTGTAGCTAGCTCA-1\n+TTGTAGCTCTCTTA-1\n+TTGTCATGGACGGA-1\n+TTTAGAGATCCTCG-1\n+TTTAGCTGATACCG-1\n+TTTAGCTGGATACC-1\n+TTTAGCTGTACTCT-1\n+TTTAGGCTCCTTTA-1\n+TTTATCCTGTTGTG-1\n+TTTCACGAGGTTCA-1\n+TTTCAGTGGAAGGC-1\n+TTTCAGTGTCACGA-1\n+TTTCAGTGTCTATC-1\n+TTTCAGTGTGCAGT-1\n+TTTCCAGAGGTGAG-1\n+TTTCGAACACCTGA-1\n+TTTCGAACTCTCAT-1\n+TTTCTACTGAGGCA-1\n+TTTCTACTTCCTCG-1\n+TTTGCATGAGAGGC-1\n+TTTGCATGCCTCAC-1\n' 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| diff -r 000000000000 -r b3c3cf813a49 test-data/genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes.tsv Wed Apr 03 11:27:08 2019 -0400 |
| b |
| b'@@ -0,0 +1,32738 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| diff -r 000000000000 -r b3c3cf813a49 test-data/pbmc3k.rds |
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| diff -r 000000000000 -r b3c3cf813a49 test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz |
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| Binary file test-data/pbmc3k_filtered_gene_bc_matrices.tar.gz has changed |
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| diff -r 000000000000 -r b3c3cf813a49 test-data/pbmc3k_sc3.rds |
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| Binary file test-data/pbmc3k_sc3.rds has changed |
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| diff -r 000000000000 -r b3c3cf813a49 test-data/scater_log.rds |
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| Binary file test-data/scater_log.rds has changed |
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| diff -r 000000000000 -r b3c3cf813a49 test-data/test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test Wed Apr 03 11:27:08 2019 -0400 |
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| @@ -0,0 +1,1 @@ + |