Galaxy |

Changeset 8:5675dc87bb8d (2020-03-04)

Previous changeset 7:60fa6080f86f (2019-11-22) Next changeset 9:e42c217a450f (2020-03-11)

Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit bf9021c853da640771202920cde38f77cdeaf368"

modified:
salmonKallistoMtxTo10x.xml

removed:
barcodes.tsv
foo.mtx/barcodes.tsv
foo.mtx/genes.tsv
foo.mtx/matrix.mtx
genes.tsv
matrix.mtx.gz

diff -r 60fa6080f86f -r 5675dc87bb8d barcodes.tsv
--- a/barcodes.tsv Fri Nov 22 11:11:16 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,41177 +0,0 @@\n-GTGTGTGTGTGTGTGT\n-ACACACACACACACAC\n-CACACACACACACACA\n-GTGAAGCTTATCAAGA\n-CTCACTTCCTAGATGA\n-GGAAGAAGTGGGGTGG\n-AAGAAGATGGGTGACC\n-GGAAGTGAAGCTTATC\n-GAAGCTTATCAAGAAG\n-GAGGAAGTGAAGCTTA\n-CAAGAAGATGGGTGAC\n-AGCTTATCAAGAAGAT\n-GCTTATCAAGAAGATG\n-AGATGGGTGACCACCT\n-GTGACTTCCTGGAGAC\n-AGAAGATGGGTGACCA\n-GTGAAATCTAGAGTAA\n-AAAGAATTGGGTGACC\n-GTGATAATGAAAGCTA\n-GCCCGAATCTGGCTTG\n-ATCAAGAAGATGGGTG\n-TGGGTGACCACCTGAC\n-AGTGAAGCTTATCAAG\n-CCCGAATCTGGCTTGG\n-GTAAAATCAAGCTGGC\n-AGGAAGTGAAGCTTAT\n-CTTATCAAGAAGATGG\n-ATGAAAGCTAAGCCTC\n-CCTAGATGAGGAAGTG\n-CTTTGACAAGCACACC\n-GAAAGAACTTGCATGT\n-GGAATATCTCTTTGAC\n-AGATGAGGAAGTGAAG\n-GACAAGCACACCCTGG\n-GACCAACTTGCGCAAG\n-GAAAGCTAAGCCTCGG\n-CAGCACTTTGGGAGGC\n-GCGGAATATCTCTTTG\n-GCAAGATGGGAGCGCC\n-GGCTAATTTCCCCATA\n-CTTGCATGTTGGTGAA\n-GTTCTGCCCGCACGGA\n-CCAACTTGCGCAAGAT\n-AAAAAAAAAAAAAAAA\n-GAAGATGGGTGACCAC\n-GGCTTGGCGGAATATC\n-GGCGGAATATCTCTTT\n-GGAAAGAACTTGCATG\n-GACTCACTTCCTAGAT\n-ATCTCTTTGACAAGCA\n-CTGGAGACTCACTTCC\n-GTGACCACGTGACCAA\n-GGTGGAAGAAGTGGGG\n-CCAGCACTTTGGGAGG\n-GAAGGAAGAAGTGGGG\n-ACTTCCTAGATGAGGA\n-GGTGGGACGACAGTGA\n-CCCATCTCTGTGACTT\n-GGTGAAAGCCATCAAA\n-GGAGACTCACTTCCTA\n-GAAGTGAAGCTTATCA\n-CTGTGACTTCCTGGAG\n-TATCAAGAAGATGGGT\n-GCACACCCTGGGAGAC\n-CTGGCTTGGCGGAATA\n-GCCCGCACGGACCCCC\n-CACGTGACCAACTTGC\n-CTTCCTAGATGAGGAA\n-AGCACACCCTGGGAGA\n-GGTGACTTCCCTGGTC\n-GCTTGGCGGAATATCT\n-CTTCCTGGAGACTCAC\n-GCTAAGCCTCGGGCTA\n-GGGAAGGAAAGAACTT\n-GTGAAGGAAGAAGTGG\n-GCCGCGCCTGCCTTTC\n-GAGCGCCCGAATCTGG\n-GGGTGACCACGTGACC\n-AAGTGAAGCTTATCAA\n-GCTAATTTCCCCATAG\n-GAAGAAGTGGGGTGGG\n-GATAATGAAAGCTAAG\n-CAAAGAATTGGGTGAC\n-AAGATGGGTGACCACC\n-GGGAGCGCCCGAATCT\n-GTTCGAGACCAGCCTG\n-GGAAAATTTAGAAATA\n-GGTGAAGGAAGAAGTG\n-GAAGGAAAGAACTTGC\n-GTGGGGTGGAAGAAGT\n-GGTGACCACGTGACCA\n-GACGACAGTGAAATCT\n-CACTTCCTAGATGAGG\n-TCCTAGATGAGGAAGT\n-CTGTAATCCCAGCACT\n-GAATTGGGTGACCACG\n-TGAAGCTTATCAAGAA\n-CTCTTTGACAAGCACA\n-CCCCCATCTCTGTGAC\n-GGACGACAGTGAAATC\n-GTGGGGTGGGACGACA\n-CTTCCCTGGTCACCAA\n-GTGACTTCCCTGGTCA\n-GCCTGTAATCCCAGCA\n-ATGTTGGTGAAGGAAG\n-AAGCCATCAAAGAATT\n-CTGCCCGCACGGACCC\n-GTTTGAGACCAGCCTG\n-GGGGTGGAAGAAGTGG\n-GACTTCCTGGAGACTC\n-GTCTATCTATCTGGCT\n-GAAATCTAGAGTAAAA\n-GTGGAAGAAGTGGGGT\n-GAAGAAGTGGGGTGGA\n-CATCTGTCTATCTATC\n-GTGAAAGCCATCAAAG\n-GGAGCGCCCGAATCTG\n-CAAGCACACCCTGGGA\n-GTTCAAGACCAGCCTG\n-GTGACCAACTTGCGCA\n-GGGAGACAGTGATAAT\n-GCGCAAGATGGGAGCG\n-GGAAGGAAAGAACTTG\n-GTAATCCCAGCACTTT\n-ACTTCCTGGAGACTCA\n-GTTTAAATGACTGTGC\n-GATGGGAGCGCCCGAA\n-CTGGGTTCTGCCCGCA\n-CTTGGCGGAATATCTC\n-CTGGCTGGCAGGGAAG\n-ATCAAAGAATTGGGTG\n-GCCGTGGGGTGACTTC\n-GATGAGGAAGTGAAGC\n-CTTCAATCTCTTGCAC\n-ATGAGGAAGTGAAGCT\n-GAGACAGTGATAATGA\n-GTTAAGCGTGCATAAG\n-GAAAGCCATCAAAGAA\n-GGGACGACAGTGAAAT\n-GTTAACTTCCAATTTA\n-AAAGAATTCACCCCAC\n-GTCAGGAGTTCGAGAC\n-GCCCTGGGTTCTGCCC\n-AAGAAGTGGGGTGGGA\n-GACCACGTGACCAACT\n-AAAGAACTTGCATGTT\n-GGATCTTCATGCCCTG\n-GGAGACAGTGATAATG\n-TTATCAAGAAGATGGG\n-CTAGATGAGGAAGTGA\n-CCTGCCTTTCCCATCT\n-GGCCGCGCCTGCCTTT\n-GGAAGCCCCAACGGGA\n-GATCTTCATGCCCTGG\n-GAACTTGCATGTTGGT\n-GACAGTGATAATGAAA\n-CCTGGAGACTCACTTC\n-AGAACTTGCATGTTGG\n-GTGACTTCATTGAGAC\n-GCCTCGGGCTAATTTC\n-CAGTGATAATGAAAGC\n-GCCATCAAAGAATTGG\n-AGGAAGAAGTGGGGTG\n-GGCAGGGAAGGAAAGA\n-ACTTGCGCAAGATGGG\n-GTCAGATTTGAACTCT\n-CTTGCGCAAGATGGGA\n-CTGGCAGGGAAGGAAA\n-CTAATTTCCCCATAGC\n-CGAATCTGGCTTGGCG\n-GGGCTAATTTCCCCAT\n-GTTGGTGAAGGAAGAA\n-CTATCTATCTGGCTGG\n-AATGAAAGCTAAGCCT\n-AATCCCAGCACTTTGG\n-TTTTTTTTTTTTTTTT\n-GGGAAAATTTAGAAAT\n-GCAAAGAATTCACCCC\n-AAGCTTATCAAGAAGA\n-CTTCAGGCTCCTGGGC\n-CTAAGCCTCGGGCTAA\n-GTGCTGGTCTGTGTGC\n-GGCTGGCAGGGAAGGA\n-ATGGGAGCGCCCGAAT\n-GGCTCATTCATTTCTC\n-GAGACACATTACCTGA\n-CTAGAGTAAAATCAAG\n-GGGTGGAAGAAGTGGG\n-CCCACATTAGGCTTAA\n-CCTGGGTTCTGCCCGC\n-AATTGGGTGACCACGT\n-TGACAAGCACACCCTG\n-GAGCAGGTGAAAGCCA\n-ACAAGCACACCCTGGG\n-GAAGTGGGGTGGGACG\n-ATCTCTGTGACTTCCT\n-AGCTAAGCCTCGGGCT\n-GGTCAGTGGAAGCCCC\n-CTGGGAGACAGTGATA\n-AGTTAACTTCCAATTT\n-GGGGTGGGACGACAGT\n-GTCCTGCAGGCTGTAA\n-GGAAATTTGTTATAAT\n-CCTCGGGCTAATTTCC\n-CAAAGAACTACTGACA\n-TCTTTGACAAGCACAC\n-CCTGAATGAGCAGGTG\n-CCGAATCTGGCTTGGC\n-CCCTGGGAGACAGTGA\n-GGCCCTTTTGGATCTT\n-GACCAGCCTGGCCAAC\n-GAAAAGTCCTAATAGT\n-GACCCCCATCTCTGTG\n-ATCAAGCTGGCCCAAG\n-AGACTCACTTCCTAGA\n-ACTAAAAATACAAAAA\n-GAAGTGGGGTGGAAGA\n-GAAGAATTCACAAAAA\n-ATAGCCGTGGGGTGAC\n-AAATCAAGCTGGCCCA\n-TATCTATCTGGCTGGC\n-'..b'GT\n-AAACTTTCAAATCCTT\n-AAACTTCTTGAATAAA\n-AAACTTCAGTCATGAT\n-AAACTTAGCAACTTGG\n-AAACTGTGTACATAAC\n-AAACTGGTACCCGTTG\n-AAACTGGATACTGCAT\n-AAACTGCTTTTGATCT\n-AAACTGCTGGGGCAAT\n-AAACTGCAGTGTCCGT\n-AAACTGATGTCTTTTC\n-AAACTGAGTACTTGGA\n-AAACTCTGGGCATTTC\n-AAACTCCAGCCCACTG\n-AAACTCATTAGTTTGG\n-AAACTCATACCTGTAT\n-AAACTATTTGTCTTTC\n-AAACTATTTGGGATAT\n-AAACTAGGAGAATGGG\n-AAACTAGATCTAGGAA\n-AAACGTGTTTTTTAAA\n-AAACGTGTGAAGGAAA\n-AAACGTACCCAGGCCC\n-AAACGGGCCCTCAAAT\n-AAACGGATTGGCCTAA\n-AAACGGACTTTTCATT\n-AAACGCAGTGTGGGAA\n-AAACGATTATGTACTC\n-AAACGATGAGACGTGC\n-AAACCTTTTTGTCTTT\n-AAACCTTCAGAAATAG\n-AAACCTTACATGTGTA\n-AAACCTAGGACCAAAG\n-AAACCTACCAAAAAGG\n-AAACCTAAATATTTAC\n-AAACCCTCATTCACAC\n-AAACCCCGATCCTTTG\n-AAACCCCCATAAATAG\n-AAACCCATTATGTAAT\n-AAACCCACATTTAAGG\n-AAACCATCCATCAATT\n-AAACCATCATTCTCAG\n-AAACCAAGCGAGGCCA\n-AAACCAAATCAGTTCT\n-AAACATTTTTGAGATA\n-AAACATTTCAAAGTTT\n-AAACATTTAAATACAA\n-AAACATTCAAGAAAAC\n-AAACATGTGCTGTGTC\n-AAACATGGTGGCCAAA\n-AAACATCTTCTGTAGC\n-AAACATCCACTTAAGT\n-AAACATAACCAGCCAT\n-AAACAGGTGTCAGGCT\n-AAACAGCTTCCTGAAT\n-AAACAGCTGTACTTTT\n-AAACAGCTGGAGGATG\n-AAACAGCTCTACTCCA\n-AAACACTTACTGCCAG\n-AAACACCCTTTGTTGA\n-AAACACAGTGAATTTG\n-AAACACAGCAGTTCTT\n-AAACACAGAACCTCAG\n-AAACACACACCAAACA\n-AAACAATGATTTTAAT\n-AAACAAGACTCCAGTG\n-AAACAACTTCTCAGAT\n-AAACAAATTTGCCGTG\n-AAACAAAGGATCTGGG\n-AAACAAAGACTGGAGA\n-AAACAAACCACCTGAC\n-AAACAAACAGGCCTCT\n-AAACAAACAATCCAGA\n-AAACAAAAAGAGGAGC\n-AAACAAAAACCGGCAC\n-AAACAAAAAAAAAATA\n-AAAATTTTTTTTTTGT\n-AAAATTTTTAGAACTT\n-AAAATTTCCATTGTAG\n-AAAATTTAAATACAAT\n-AAAATTGTGAAAGTAA\n-AAAATTGCACACACTC\n-AAAATTACACCTGGCA\n-AAAATGTTTAAATTAA\n-AAAATGTGACCCACAG\n-AAAATGGTGAAACCCC\n-AAAATGCAAAAATTAG\n-AAAATGATGGCAGTGT\n-AAAATGATCCAGACTA\n-AAAATGATCAAGCCTT\n-AAAATGAATCTTTCAA\n-AAAATCTTTTAATACA\n-AAAATCTTCCAGTTAC\n-AAAATCTGCCACGATT\n-AAAATCGAGCGGGCCA\n-AAAATCCTTTTTTGTA\n-AAAATCCGGGCTGCTG\n-AAAATCCATTTCACTA\n-AAAATCCAGAAGGTAT\n-AAAATCAGCTACTAGA\n-AAAATCAGCCAGGTGT\n-AAAATCAATGTGAAAA\n-AAAATATTTGAAGAAG\n-AAAATAGTAAAATATA\n-AAAATAGCTTTTGCCG\n-AAAATACCAAGTCTCC\n-AAAATACAAAAAAAAA\n-AAAATAATGTGAGGCG\n-AAAATAATGCTGTTCT\n-AAAATAACTTCATTGT\n-AAAATAAAACAATAAA\n-AAAAGTTGTTAAACAA\n-AAAAGTTATTACACTA\n-AAAAGTTATCCTACAC\n-AAAAGTCTCCAGTCTG\n-AAAAGTAGTAAATAGT\n-AAAAGTAACCTTGGCT\n-AAAAGGTTGAGCCAAA\n-AAAAGGTGGGTGAATT\n-AAAAGGTCAAGGCCTT\n-AAAAGGGGACGATTGC\n-AAAAGGGATTACCCAA\n-AAAAGGCTAAAACTAC\n-AAAAGGCAGCAGCTAC\n-AAAAGGCAGAGCCCTG\n-AAAAGGCAAAGGCTAA\n-AAAAGGAGATCTTTAA\n-AAAAGGACACTTCTGA\n-AAAAGGAAGAAGAATA\n-AAAAGCTTTTGTTTTC\n-AAAAGCTGGGAACCTT\n-AAAAGCTGCTGCTCCT\n-AAAAGCTCCGCAACAA\n-AAAAGCGCTGCAGTAG\n-AAAAGCCTGTGGCTTC\n-AAAAGCCACTGGGGAC\n-AAAAGATTCTTTCCAA\n-AAAAGATCTGCTAGAA\n-AAAAGAGTGCTGAATT\n-AAAAGAGCTTAACAGG\n-AAAAGAGAAATATGAG\n-AAAAGACTATTGTGCC\n-AAAAGAATGTCTGTTT\n-AAAAGAAGCCATTGCT\n-AAAAGAAGAAAACGAA\n-AAAACTTTTTGGTGCT\n-AAAACTTTCAAGTGAA\n-AAAACTTGGTGTGGGG\n-AAAACTTAAGAATCCC\n-AAAACTGTCGTCAATA\n-AAAACTGCGAGCCAGC\n-AAAACTGAAACTGTGG\n-AAAACTATCCAGTGAT\n-AAAACTACTCCAGTGG\n-AAAACTACCAGTTCTT\n-AAAACTAATGTAAACT\n-AAAACTAATCGTCCCA\n-AAAACTAACAGATGAA\n-AAAACGTAATGAGGAT\n-AAAACCTTTTATGACA\n-AAAACCTTGCATCCTA\n-AAAACCTGCACTTGTT\n-AAAACCTAGACCTTGA\n-AAAACCATGGTCCCCC\n-AAAACCAGAGTCATCT\n-AAAACCAAGCGAGGCC\n-AAAACATTATTGAGGA\n-AAAACAGCACAAAAAA\n-AAAACACTTCCTTGGA\n-AAAACAAGGACTGCAG\n-AAAACAACAACATAAA\n-AAAACAACAACAAAGA\n-AAAACAAATTTGCCGT\n-AAAACAAAGTTGATTG\n-AAAACAAACAATCCAG\n-AAAACAAAACAAAACA\n-AAAAATTGTTCAACCT\n-AAAAATTGCACACACT\n-AAAAATTCAGTTGCTT\n-AAAAATTAGCCTTGCG\n-AAAAATGTTTTCCCCA\n-AAAAATGTTTAAAATG\n-AAAAATGAACCCAAAC\n-AAAAATAAGCAAAAGC\n-AAAAATAAGAGGCGAT\n-AAAAATAAGAACCTGG\n-AAAAAGTCCTAATAGT\n-AAAAAGTCCAGTAACC\n-AAAAAGGGTGCAGACG\n-AAAAAGGGGTTTCTTT\n-AAAAAGCTCCAGCCCA\n-AAAAAGCCGTACAAAA\n-AAAAAGATATTGTTGT\n-AAAAAGAAAGAAGCCA\n-AAAAAGAAAAAGAAGA\n-AAAAACGCGAAATTCT\n-AAAAACAATCTTATTC\n-AAAAACAACTTCTCAG\n-AAAAACAAAGCACATG\n-AAAAACAAAAAGAAAT\n-AAAAAATTTTGCATTA\n-AAAAAATTGTATTGAA\n-AAAAAATTCCCCCCAT\n-AAAAAATTCAAATGCA\n-AAAAAATGCAGGTTGT\n-AAAAAATCTCTTTTTT\n-AAAAAATCTATCATGT\n-AAAAAATAGTCAATAG\n-AAAAAAGGCAGCAGCT\n-AAAAAAGGAGAAAGCC\n-AAAAAAGAATTCCACT\n-AAAAAAGAAATGAAAA\n-AAAAAACTTCCTACCA\n-AAAAAACTCGAGGACT\n-AAAAAACGGATCACCG\n-AAAAAACCGTCGAGAT\n-AAAAAACCAAGTAGTG\n-AAAAAACACAAAAAAT\n-AAAAAACAAGACTAAA\n-AAAAAAAGTTGGTGAT\n-AAAAAAAGCCATGAAG\n-AAAAAAACAGAGATGG\n'

diff -r 60fa6080f86f -r 5675dc87bb8d foo.mtx/barcodes.tsv
--- a/foo.mtx/barcodes.tsv Fri Nov 22 11:11:16 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 60fa6080f86f -r 5675dc87bb8d foo.mtx/genes.tsv
--- a/foo.mtx/genes.tsv Fri Nov 22 11:11:16 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,32919 +0,0 @@\n-ERCC-00002\tERCC-00002\n-ERCC-00003\tERCC-00003\n-ERCC-00004\tERCC-00004\n-ERCC-00009\tERCC-00009\n-ERCC-00012\tERCC-00012\n-ERCC-00013\tERCC-00013\n-ERCC-00014\tERCC-00014\n-ERCC-00016\tERCC-00016\n-ERCC-00017\tERCC-00017\n-ERCC-00019\tERCC-00019\n-ERCC-00022\tERCC-00022\n-ERCC-00024\tERCC-00024\n-ERCC-00025\tERCC-00025\n-ERCC-00028\tERCC-00028\n-ERCC-00031\tERCC-00031\n-ERCC-00033\tERCC-00033\n-ERCC-00034\tERCC-00034\n-ERCC-00035\tERCC-00035\n-ERCC-00039\tERCC-00039\n-ERCC-00040\tERCC-00040\n-ERCC-00041\tERCC-00041\n-ERCC-00042\tERCC-00042\n-ERCC-00043\tERCC-00043\n-ERCC-00044\tERCC-00044\n-ERCC-00046\tERCC-00046\n-ERCC-00048\tERCC-00048\n-ERCC-00051\tERCC-00051\n-ERCC-00053\tERCC-00053\n-ERCC-00054\tERCC-00054\n-ERCC-00057\tERCC-00057\n-ERCC-00058\tERCC-00058\n-ERCC-00059\tERCC-00059\n-ERCC-00060\tERCC-00060\n-ERCC-00061\tERCC-00061\n-ERCC-00062\tERCC-00062\n-ERCC-00067\tERCC-00067\n-ERCC-00069\tERCC-00069\n-ERCC-00071\tERCC-00071\n-ERCC-00073\tERCC-00073\n-ERCC-00074\tERCC-00074\n-ERCC-00075\tERCC-00075\n-ERCC-00076\tERCC-00076\n-ERCC-00077\tERCC-00077\n-ERCC-00078\tERCC-00078\n-ERCC-00079\tERCC-00079\n-ERCC-00081\tERCC-00081\n-ERCC-00083\tERCC-00083\n-ERCC-00084\tERCC-00084\n-ERCC-00085\tERCC-00085\n-ERCC-00086\tERCC-00086\n-ERCC-00092\tERCC-00092\n-ERCC-00095\tERCC-00095\n-ERCC-00096\tERCC-00096\n-ERCC-00097\tERCC-00097\n-ERCC-00098\tERCC-00098\n-ERCC-00099\tERCC-00099\n-ERCC-00104\tERCC-00104\n-ERCC-00108\tERCC-00108\n-ERCC-00109\tERCC-00109\n-ERCC-00111\tERCC-00111\n-ERCC-00112\tERCC-00112\n-ERCC-00113\tERCC-00113\n-ERCC-00116\tERCC-00116\n-ERCC-00117\tERCC-00117\n-ERCC-00120\tERCC-00120\n-ERCC-00123\tERCC-00123\n-ERCC-00126\tERCC-00126\n-ERCC-00130\tERCC-00130\n-ERCC-00131\tERCC-00131\n-ERCC-00134\tERCC-00134\n-ERCC-00136\tERCC-00136\n-ERCC-00137\tERCC-00137\n-ERCC-00138\tERCC-00138\n-ERCC-00142\tERCC-00142\n-ERCC-00143\tERCC-00143\n-ERCC-00144\tERCC-00144\n-ERCC-00145\tERCC-00145\n-ERCC-00147\tERCC-00147\n-ERCC-00148\tERCC-00148\n-ERCC-00150\tERCC-00150\n-ERCC-00154\tERCC-00154\n-ERCC-00156\tERCC-00156\n-ERCC-00157\tERCC-00157\n-ERCC-00158\tERCC-00158\n-ERCC-00160\tERCC-00160\n-ERCC-00162\tERCC-00162\n-ERCC-00163\tERCC-00163\n-ERCC-00164\tERCC-00164\n-ERCC-00165\tERCC-00165\n-ERCC-00168\tERCC-00168\n-ERCC-00170\tERCC-00170\n-ERCC-00171\tERCC-00171\n-ENSG00000223972\tENSG00000223972\n-ENSG00000227232\tENSG00000227232\n-ENSG00000268020\tENSG00000268020\n-ENSG00000240361\tENSG00000240361\n-ENSG00000186092\tENSG00000186092\n-ENSG00000233750\tENSG00000233750\n-ENSG00000268903\tENSG00000268903\n-ENSG00000269981\tENSG00000269981\n-ENSG00000279928\tENSG00000279928\n-ENSG00000279457\tENSG00000279457\n-ENSG00000228463\tENSG00000228463\n-ENSG00000236679\tENSG00000236679\n-ENSG00000237094\tENSG00000237094\n-ENSG00000269732\tENSG00000269732\n-ENSG00000233653\tENSG00000233653\n-ENSG00000250575\tENSG00000250575\n-ENSG00000230021\tENSG00000230021\n-ENSG00000225972\tENSG00000225972\n-ENSG00000225630\tENSG00000225630\n-ENSG00000237973\tENSG00000237973\n-ENSG00000229344\tENSG00000229344\n-ENSG00000240409\tENSG00000240409\n-ENSG00000248527\tENSG00000248527\n-ENSG00000198744\tENSG00000198744\n-ENSG00000268663\tENSG00000268663\n-ENSG00000229376\tENSG00000229376\n-ENSG00000228327\tENSG00000228327\n-ENSG00000285268\tENSG00000285268\n-ENSG00000230092\tENSG00000230092\n-ENSG00000234711\tENSG00000234711\n-ENSG00000283040\tENSG00000283040\n-ENSG00000187634\tENSG00000187634\n-ENSG00000188976\tENSG00000188976\n-ENSG00000187961\tENSG00000187961\n-ENSG00000187583\tENSG00000187583\n-ENSG00000187642\tENSG00000187642\n-ENSG00000188290\tENSG00000188290\n-ENSG00000187608\tENSG00000187608\n-ENSG00000231702\tENSG00000231702\n-ENSG00000188157\tENSG00000188157\n-ENSG00000217801\tENSG00000217801\n-ENSG00000237330\tENSG00000237330\n-ENSG00000131591\tENSG00000131591\n-ENSG00000162571\tENSG00000162571\n-ENSG00000186891\tENSG00000186891\n-ENSG00000186827\tENSG00000186827\n-ENSG00000078808\tENSG00000078808\n-ENSG00000176022\tENSG00000176022\n-ENSG00000184163\tENSG00000184163\n-ENSG00000160087\tENSG00000160087\n-ENSG00000162572\tENSG00000162572\n-ENSG00000131584\tENSG00000131584\n-ENSG00000169972\tENSG00000169972\n-ENSG00000127054\tENSG00000127054\n-ENSG00000224051\tENSG00000224051\n-ENSG00000169962\tENSG00000169962\n-ENSG0000010740'..b'32429\n-ENSG00000124302\tENSG00000124302\n-ENSG00000153885\tENSG00000153885\n-ENSG00000239253\tENSG00000239253\n-ENSG00000249987\tENSG00000249987\n-ENSG00000186008\tENSG00000186008\n-ENSG00000270849\tENSG00000270849\n-ENSG00000257103\tENSG00000257103\n-ENSG00000166398\tENSG00000166398\n-ENSG00000257074\tENSG00000257074\n-ENSG00000105220\tENSG00000105220\n-ENSG00000266953\tENSG00000266953\n-ENSG00000126249\tENSG00000126249\n-ENSG00000126261\tENSG00000126261\n-ENSG00000142279\tENSG00000142279\n-ENSG00000239210\tENSG00000239210\n-ENSG00000248830\tENSG00000248830\n-ENSG00000205209\tENSG00000205209\n-ENSG00000271049\tENSG00000271049\n-ENSG00000269811\tENSG00000269811\n-ENSG00000089335\tENSG00000089335\n-ENSG00000197841\tENSG00000197841\n-ENSG00000153896\tENSG00000153896\n-ENSG00000270281\tENSG00000270281\n-ENSG00000271666\tENSG00000271666\n-ENSG00000270624\tENSG00000270624\n-ENSG00000168661\tENSG00000168661\n-ENSG00000180884\tENSG00000180884\n-ENSG00000089351\tENSG00000089351\n-ENSG00000105711\tENSG00000105711\n-ENSG00000105707\tENSG00000105707\n-ENSG00000285526\tENSG00000285526\n-ENSG00000089356\tENSG00000089356\n-ENSG00000153902\tENSG00000153902\n-ENSG00000266964\tENSG00000266964\n-ENSG00000221946\tENSG00000221946\n-ENSG00000089327\tENSG00000089327\n-ENSG00000177558\tENSG00000177558\n-ENSG00000262497\tENSG00000262497\n-ENSG00000105699\tENSG00000105699\n-ENSG00000105698\tENSG00000105698\n-ENSG00000105697\tENSG00000105697\n-ENSG00000105695\tENSG00000105695\n-ENSG00000012124\tENSG00000012124\n-ENSG00000126266\tENSG00000126266\n-ENSG00000185897\tENSG00000185897\n-ENSG00000126251\tENSG00000126251\n-ENSG00000268222\tENSG00000268222\n-ENSG00000283479\tENSG00000283479\n-ENSG00000126262\tENSG00000126262\n-ENSG00000188508\tENSG00000188508\n-ENSG00000161249\tENSG00000161249\n-ENSG00000189001\tENSG00000189001\n-ENSG00000105679\tENSG00000105679\n-ENSG00000105677\tENSG00000105677\n-ENSG00000105675\tENSG00000105675\n-ENSG00000283758\tENSG00000283758\n-ENSG00000249115\tENSG00000249115\n-ENSG00000126254\tENSG00000126254\n-ENSG00000105672\tENSG00000105672\n-ENSG00000126267\tENSG00000126267\n-ENSG00000105668\tENSG00000105668\n-ENSG00000267190\tENSG00000267190\n-ENSG00000011590\tENSG00000011590\n-ENSG00000272333\tENSG00000272333\n-ENSG00000126246\tENSG00000126246\n-ENSG00000267120\tENSG00000267120\n-ENSG00000161265\tENSG00000161265\n-ENSG00000205155\tENSG00000205155\n-ENSG00000188223\tENSG00000188223\n-ENSG00000267796\tENSG00000267796\n-ENSG00000004776\tENSG00000004776\n-ENSG00000167595\tENSG00000167595\n-ENSG00000004777\tENSG00000004777\n-ENSG00000225872\tENSG00000225872\n-ENSG00000250799\tENSG00000250799\n-ENSG00000161270\tENSG00000161270\n-ENSG00000126259\tENSG00000126259\n-ENSG00000105290\tENSG00000105290\n-ENSG00000167604\tENSG00000167604\n-ENSG00000126264\tENSG00000126264\n-ENSG00000011600\tENSG00000011600\n-ENSG00000126243\tENSG00000126243\n-ENSG00000267113\tENSG00000267113\n-ENSG00000205138\tENSG00000205138\n-ENSG00000181392\tENSG00000181392\n-ENSG00000239382\tENSG00000239382\n-ENSG00000105270\tENSG00000105270\n-ENSG00000161277\tENSG00000161277\n-ENSG00000075702\tENSG00000075702\n-ENSG00000105261\tENSG00000105261\n-ENSG00000105258\tENSG00000105258\n-ENSG00000105254\tENSG00000105254\n-ENSG00000126247\tENSG00000126247\n-ENSG00000161281\tENSG00000161281\n-ENSG00000267005\tENSG00000267005\n-ENSG00000196357\tENSG00000196357\n-ENSG00000167635\tENSG00000167635\n-ENSG00000142065\tENSG00000142065\n-ENSG00000181007\tENSG00000181007\n-ENSG00000267142\tENSG00000267142\n-ENSG00000186017\tENSG00000186017\n-ENSG00000267091\tENSG00000267091\n-ENSG00000254004\tENSG00000254004\n-ENSG00000186020\tENSG00000186020\n-ENSG00000161298\tENSG00000161298\n-ENSG00000197808\tENSG00000197808\n-ENSG00000189042\tENSG00000189042\n-ENSG00000267041\tENSG00000267041\n-ENSG00000197863\tENSG00000197863\n-ENSG00000251247\tENSG00000251247\n-ENSG00000185869\tENSG00000185869\n-ENSG00000243297\tENSG00000243297\n-ENSG00000198453\tENSG00000198453\n-ENSG00000197050\tENSG00000197050\n-ENSG00000275547\tENSG00000275547\n-ENSG00000267360\tENSG00000267360\n-ENSG00000196967\tENSG00000196967\n-ENSG00000245680\tENSG00000245680\n-ENSG00000188283\tENSG00000188283\n-ENSG00000181666\tENSG00000181666\n-ENSG00000189164\tENSG00000189164\n'

diff -r 60fa6080f86f -r 5675dc87bb8d foo.mtx/matrix.mtx
--- a/foo.mtx/matrix.mtx Fri Nov 22 11:11:16 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,427534 +0,0 @@\n-%%MatrixMarket matrix coordinate real general\n-%\n-35550 4409 427531\n-186 1 2.000000000000000e+00\n-216 1 1.000000000000000e+00\n-303 1 1.000000000000000e+00\n-309 1 1.000000000000000e+00\n-448 1 1.000000000000000e+00\n-457 1 1.000000000000000e+00\n-466 1 3.000000000000000e+00\n-533 1 4.000000000000000e+00\n-594 1 1.000000000000000e+00\n-641 1 1.000000000000000e+00\n-707 1 1.000000000000000e+00\n-712 1 1.000000000000000e+00\n-744 1 1.000000000000000e+00\n-768 1 1.000000000000000e+00\n-827 1 1.000000000000000e+00\n-902 1 2.000000000000000e+00\n-926 1 1.000000000000000e+00\n-939 1 2.000000000000000e+00\n-958 1 2.000000000000000e+00\n-981 1 5.000000000000000e-01\n-982 1 5.000000000000000e-01\n-1008 1 1.000000000000000e+00\n-1121 1 1.000000000000000e+00\n-1183 1 1.000000000000000e+00\n-1316 1 1.000000000000000e+00\n-1328 1 1.000000000000000e+00\n-1384 1 1.000000000000000e+00\n-1452 1 1.000000000000000e+00\n-1495 1 1.520000000000000e-04\n-1540 1 3.333330000000000e-01\n-1600 1 1.000000000000000e+00\n-1616 1 5.000000000000000e-01\n-1617 1 5.000000000000000e-01\n-1731 1 1.000000000000000e+00\n-1786 1 1.000000000000000e+00\n-1790 1 9.090900000000000e-02\n-1792 1 9.090900000000000e-02\n-1834 1 9.090900000000000e-02\n-1848 1 9.090900000000000e-02\n-1852 1 9.090900000000000e-02\n-1857 1 1.000000000000000e+00\n-1869 1 1.000000000000000e+00\n-1871 1 9.090900000000000e-02\n-1872 1 9.090900000000000e-02\n-1879 1 9.090900000000000e-02\n-1915 1 9.090900000000000e-02\n-1920 1 9.090900000000000e-02\n-1924 1 9.090900000000000e-02\n-1952 1 1.000000000000000e+00\n-2016 1 5.000000000000000e+00\n-2018 1 2.000000000000000e+00\n-2086 1 1.000000000000000e+00\n-2093 1 1.000000000000000e+00\n-2114 1 1.000000000000000e+00\n-2118 1 1.000000000000000e+00\n-2154 1 5.000000000000000e-01\n-2155 1 5.000000000000000e-01\n-2177 1 1.000000000000000e+00\n-2192 1 1.000000000000000e+00\n-2196 1 1.000000000000000e+00\n-2218 1 1.000000000000000e+00\n-2259 1 1.000000000000000e+00\n-2345 1 9.000000000000000e+00\n-2366 1 1.000000000000000e+00\n-2404 1 1.000000000000000e+00\n-2408 1 1.000000000000000e+00\n-2624 1 1.000000000000000e+00\n-2677 1 1.000000000000000e+00\n-2836 1 1.000000000000000e+00\n-2898 1 1.000000000000000e+00\n-2948 1 3.333330000000000e-01\n-2978 1 1.000000000000000e+00\n-3082 1 1.000000000000000e+00\n-3437 1 3.333330000000000e-01\n-3454 1 1.000000000000000e+00\n-3474 1 1.000000000000000e+00\n-3519 1 1.000000000000000e+00\n-3636 1 1.000000000000000e+00\n-3646 1 3.000000000000000e+00\n-3786 1 1.000000000000000e+00\n-3794 1 0.000000000000000e+00\n-3828 1 5.000000000000000e-01\n-3846 1 3.000000000000000e+00\n-3984 1 1.000000000000000e+00\n-4006 1 1.000000000000000e+00\n-4031 1 3.333330000000000e-01\n-4076 1 1.000000000000000e+00\n-4125 1 1.000000000000000e+00\n-4442 1 1.000000000000000e+00\n-4445 1 1.000000000000000e+00\n-4456 1 2.000000000000000e+00\n-4628 1 1.000000000000000e+00\n-4674 1 1.000000000000000e+00\n-4694 1 1.000000000000000e+00\n-4759 1 1.000000000000000e+00\n-4933 1 1.000000000000000e+00\n-4940 1 1.000000000000000e+00\n-5237 1 1.000000000000000e+00\n-5244 1 1.000000000000000e+00\n-5389 1 1.000000000000000e+00\n-5475 1 1.000000000000000e+00\n-5524 1 5.000000000000000e-01\n-5525 1 5.000000000000000e-01\n-5550 1 1.000000000000000e+00\n-5653 1 1.000000000000000e+00\n-5900 1 1.000000000000000e+00\n-5915 1 1.000000000000000e+00\n-5981 1 3.000000000000000e+00\n-6126 1 3.333330000000000e-01\n-6133 1 3.000000000000000e+00\n-6276 1 1.000000000000000e+00\n-6386 1 3.000000000000000e+00\n-6434 1 1.000000000000000e+00\n-6502 1 2.000000000000000e+00\n-6524 1 1.000000000000000e+00\n-6645 1 2.000000000000000e+00\n-6695 1 1.000000000000000e+00\n-6715 1 2.000000000000000e+00\n-6792 1 1.000000000000000e+00\n-6833 1 2.000000000000000e+00\n-6939 1 1.000000000000000e+00\n-7099 1 1.000000000000000e+00\n-7199 1 2.000000000000000e+00\n-7368 1 1.000000000000000e+00\n-7443 1 1.000000000000000e+00\n-7709 1 1.000000000000000e+00\n-7990 1 1.000000000000000e+00\n-8007 1 1.500000000000000e+00\n-8322 1 1.000000000000000e+00\n-8449 1 1.000000000000000e+00\n-8594 1 1.000000000000000e+00\n'..b'00000000e-01\n-6426 4407 1.000000000000000e+00\n-6744 4407 1.000000000000000e+00\n-8143 4407 9.090900000000000e-02\n-8601 4407 1.000000000000000e+00\n-9204 4407 1.000000000000000e+00\n-9407 4407 9.090900000000000e-02\n-10777 4407 1.000000000000000e+00\n-11338 4407 1.000000000000000e+00\n-11417 4407 1.000000000000000e+00\n-12331 4407 1.000000000000000e+00\n-12688 4407 9.090900000000000e-02\n-13983 4407 1.000000000000000e+00\n-14038 4407 1.000000000000000e+00\n-14240 4407 9.090900000000000e-02\n-14655 4407 2.000000000000000e+00\n-15333 4407 1.000000000000000e+00\n-17422 4407 1.000000000000000e+00\n-17594 4407 1.000000000000000e+00\n-19114 4407 1.000000000000000e+00\n-20125 4407 5.000000000000000e-01\n-20126 4407 5.000000000000000e-01\n-20993 4407 1.000000000000000e+00\n-23211 4407 9.090900000000000e-02\n-23422 4407 1.000000000000000e+00\n-23642 4407 9.090900000000000e-02\n-24217 4407 1.000000000000000e+00\n-25052 4407 1.000000000000000e+00\n-25393 4407 1.000000000000000e+00\n-26717 4407 1.000000000000000e+00\n-26999 4407 2.000000000000000e+00\n-27282 4407 1.000000000000000e+00\n-28272 4407 5.000000000000000e-01\n-28274 4407 5.000000000000000e-01\n-28449 4407 1.000000000000000e+00\n-28759 4407 1.000000000000000e+00\n-30503 4407 9.090900000000000e-02\n-31305 4407 1.000000000000000e+00\n-31957 4407 1.000000000000000e+00\n-32255 4407 1.000000000000000e+00\n-32738 4407 3.333330000000000e-01\n-34980 4407 9.090900000000000e-02\n-35511 4407 1.000000000000000e+00\n-793 4408 1.000000000000000e+00\n-1805 4408 1.000000000000000e+00\n-3437 4408 2.500000000000000e-01\n-3846 4408 1.000000000000000e+00\n-3863 4408 5.000000000000000e-01\n-4164 4408 1.000000000000000e+00\n-8415 4408 1.000000000000000e+00\n-9868 4408 1.000000000000000e+00\n-10452 4408 1.000000000000000e+00\n-14655 4408 2.000000000000000e+00\n-14756 4408 1.000000000000000e+00\n-19114 4408 2.000000000000000e+00\n-19388 4408 5.000000000000000e-01\n-19395 4408 1.000000000000000e+00\n-20287 4408 1.000000000000000e+00\n-20821 4408 1.000000000000000e+00\n-21317 4408 1.000000000000000e+00\n-22161 4408 5.000000000000000e-01\n-23189 4408 1.000000000000000e+00\n-24312 4408 2.500000000000000e-01\n-24556 4408 1.000000000000000e+00\n-25813 4408 1.000000000000000e+00\n-26717 4408 1.000000000000000e+00\n-28436 4408 1.000000000000000e+00\n-29393 4408 2.500000000000000e-01\n-29619 4408 1.000000000000000e+00\n-29816 4408 1.000000000000000e+00\n-29913 4408 2.500000000000000e-01\n-30849 4408 5.000000000000000e-01\n-30850 4408 5.000000000000000e-01\n-32549 4408 1.000000000000000e+00\n-33389 4408 5.000000000000000e-01\n-33485 4408 1.000000000000000e+00\n-33691 4408 1.000000000000000e+00\n-35507 4408 1.000000000000000e+00\n-35508 4408 1.000000000000000e+00\n-169 4409 1.000000000000000e+00\n-373 4409 1.000000000000000e+00\n-2863 4409 1.000000000000000e+00\n-2875 4409 1.000000000000000e+00\n-3846 4409 1.000000000000000e+00\n-5900 4409 1.000000000000000e+00\n-6177 4409 1.000000000000000e+00\n-7356 4409 1.000000000000000e+00\n-9564 4409 3.333330000000000e-01\n-10033 4409 1.000000000000000e+00\n-10131 4409 1.000000000000000e+00\n-11313 4409 1.000000000000000e+00\n-14655 4409 1.000000000000000e+00\n-16220 4409 3.000000000000000e+00\n-17749 4409 1.000000000000000e+00\n-18791 4409 1.000000000000000e+00\n-18817 4409 1.000000000000000e+00\n-20125 4409 5.000000000000000e-01\n-20126 4409 5.000000000000000e-01\n-20504 4409 5.000000000000000e-01\n-21176 4409 1.000000000000000e+00\n-21943 4409 1.000000000000000e+00\n-22603 4409 5.000000000000000e-01\n-23407 4409 1.000000000000000e+00\n-24136 4409 1.000000000000000e+00\n-24298 4409 1.000000000000000e+00\n-25426 4409 1.000000000000000e+00\n-26069 4409 1.000000000000000e+00\n-26099 4409 1.000000000000000e+00\n-29048 4409 3.333330000000000e-01\n-29049 4409 3.333330000000000e-01\n-29790 4409 1.000000000000000e+00\n-30023 4409 5.000000000000000e-01\n-30024 4409 5.000000000000000e-01\n-32151 4409 1.000000000000000e+00\n-32878 4409 1.000000000000000e+00\n-33279 4409 1.000000000000000e+00\n-33348 4409 2.000000000000000e+00\n-33691 4409 1.000000000000000e+00\n-35516 4409 1.000000000000000e+00\n'

diff -r 60fa6080f86f -r 5675dc87bb8d genes.tsv
--- a/genes.tsv Fri Nov 22 11:11:16 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,32919 +0,0 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diff -r 60fa6080f86f -r 5675dc87bb8d matrix.mtx.gz

Binary file matrix.mtx.gz has changed

diff -r 60fa6080f86f -r 5675dc87bb8d salmonKallistoMtxTo10x.xml
--- a/salmonKallistoMtxTo10x.xml Fri Nov 22 11:11:16 2019 -0500
+++ b/salmonKallistoMtxTo10x.xml Wed Mar 04 06:44:57 2020 -0500

[

@@ -1,8 +1,8 @@
-<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy3">
+<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy4" profile="18.01">
     <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
     <requirements>
-      <requirement type="package">scipy</requirement>
-      <requirement type="package">pandas</requirement>
+      <requirement type="package" version="1.4.1">scipy</requirement>
+      <requirement type="package" version="1.0.1">pandas</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         file $mtx_file | grep 'gzip compressed' > /dev/null;
@@ -27,7 +27,7 @@
         <data name="barcodes_out" format="tabular" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/>
         <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
     </outputs>
-
+
     <help><![CDATA[
.. class:: infomark

@@ -39,13 +39,13 @@

MTX and row and gene labels from the relevant tool. For Alevin this will be

- * Matrix file: quants_mat.mtx.gz
+ * Matrix file: quants_mat.mtx.gz
  * Genes file: quants_mat_cols.txt
  * Barcodes file: quants_mat_rows.txt

For Kallisto it will be:

- * Matrix file: [name].mtx.gz
+ * Matrix file: [name].mtx.gz
  * Genes file: [name].genes.txt
  * Barcodes file: [name].barcodes.txt