| Previous changeset 0:32e1bfc6b7b2 (2018-08-15) Next changeset 2:5c4bca9dd4a2 (2019-01-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a |
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modified:
scpipe.xml tool_data_table_conf.xml.test |
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added:
test-data/cached_locally/all_fasta.loc test-data/cached_locally/mm10_MT.fa |
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| diff -r 32e1bfc6b7b2 -r 4ec6717872b1 scpipe.xml --- a/scpipe.xml Wed Aug 15 13:54:40 2018 -0400 +++ b/scpipe.xml Fri Aug 17 08:22:49 2018 -0400 |
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| @@ -28,7 +28,7 @@ #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier)) ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' && #else: - #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier)) + #set $fasta_name = os.path.basename(str($ref_fasta.ref_fa_builtin.fields.path)) ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' && #end if @@ -156,12 +156,12 @@ help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No"> </param> <section name="adv" title="Advanced Options"> - <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" /> - <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" /> - <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" /> - <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" /> - <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" /> - <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" /> + <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" /> + <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" /> + <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" /> + <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" /> + <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" /> + <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" /> <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" /> <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" /> <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" /> @@ -206,6 +206,23 @@ </assert_contents> </output> </test> + <!-- Ensure built-in fasta works --> + <test> + <param name="fasta_source" value="cached"/> + <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> + <param name="paired_format_selector" value="paired" /> + <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/> + <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/> + <param name="us" value="-1"/> + <param name="max_reads" value="5000000"/> + <param name="min_count" value="100"/> + <param name="report" value="False" /> + <output name="out_matrix" > + <assert_contents> + <has_text text="ENSMUSG00000064351" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark |
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| diff -r 32e1bfc6b7b2 -r 4ec6717872b1 test-data/cached_locally/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/all_fasta.loc Fri Aug 17 08:22:49 2018 -0400 |
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| @@ -0,0 +1,1 @@ +mm10 mm10 mm10_Fasta ${__HERE__}/mm10_MT.fa |
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| diff -r 32e1bfc6b7b2 -r 4ec6717872b1 test-data/cached_locally/mm10_MT.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/mm10_MT.fa Fri Aug 17 08:22:49 2018 -0400 |
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| @@ -0,0 +1,100 @@ +>MT +GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCC +CATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCA +AACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTA +TCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA +GTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAA +ATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAA +CGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTG +TTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAG +ACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTA +ACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTA +CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCAT +CTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGT +AAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAA +ATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAA +GGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGC +ACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACA +TCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAA +TAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCA +ATGAACACTCTGAACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATAT +AAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCT +ATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAACAAGCAAAGA +TTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAACTTCTAACTAAAAGAATTAC +AGCTAGAAACCCCGAAACCAAACGAGCTACCTAAAAACAATTTTATGAATCAACTCGTCT +ATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGA +TAGCTGGTTACCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAA +AATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAACGGAAAAA +ACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCATTGTAGGCCTAAAAGCAGCC +ACCAATAAAGAAAGCGTTCAAGCTCAACATAAAATTTCAATTAATTCCATAATTTACACC +AACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTAT +GAGTAACAAGAATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTT +AGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAACTTCTCTGTT +AACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACA +AGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACAAGTATTAGAGGCACTGC +CTGCCCAGTGACTAAAGTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATC +ACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTAAACGAGGGTCCAACTGTCTCTTAT +CTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGGCTGAAATATAATAATAAGACGAGAA +GACCCTATGGAGCTTAAATTATATAACTTATCTATTTAATTTATTAAACCTAATGGCCCA +AAAACTATAGTATAAGTTTGAAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTC +CGAATGATTATAACCTAGACTTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAG +ATATATTTTGATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAG +TTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCAATGGTGTA +GAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACC +GGAGCAATCCAGGTCGGTTTCTATCTATTTACGATTTCTCCCAGTACGAAAGGACAAGAG +AAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAA +AATATATACGTACACCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATT +GCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTA +TTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAACATTAGTAG +AACGCAAAATCTTAGGGTACATACAACTACGAAAAGGCCCTAACATTGTTGGTCCATACG +GCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTT +TAACAACCTCTATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAA +GTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTAGGGATTTTAT +TTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAA +ACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAG +TAACCATAGCTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAA +CACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAA +TATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAG +AATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCT +TTATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAG +GACCCCTATACTATATCAATTTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTC +TACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATC +AACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTATGTATGTGAC +ATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATAGAAATATGTCTGAT +AAAAGAATTACTTTGATAGAGTAAATTATAGAGGTTCAAGCCCTCTTATTTCTAGGACAA +TAGGAATTGAACCTACACTTAAGAATTCAAAATTCTCCGTGCTACCTAAACACCTTATCC +TAATAGTAAGGTCAGCTAATTAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAAT +CCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCACAATCTTCTTAGG +TCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCCTGGAATTCAG +CCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGC +AACAAAATACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACT +CAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACGGTCTTATCCTTAA +CATAACATTAATAGCCCTATCCATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACC +AGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAAT +TGCTCCCCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTACTATCATTTTAAT +ACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGACTTAACCAAACACAAATACG +AAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTA +CAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATT +CATAGCACTTATACTAAATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAA +AACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACC +ACTAACAGGATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCT +AATTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCT +AATTTATTCCACTTCACTAACAATATTTCCAACCAACAATAACTCAAAAATAATAACTCA +CCAAACAAAAACTAAACCCAACCTAATATTTTCCACCCTAGCTATCATAAGCACAATAAC +CCTACCCCTAGCCCCCCAACTAATTACCTAGAAGTTTAGGATATACTAGTCCGCGAGCCT +TCAAAGCCCTAAGAAAACACACAAGTTTAACTTCTGATAAGGACTGTAAGACTTCATCCT +ACATCTATTGAATGCAAATCAATTGCTTTAATTAAGCTAAGACCTCAACTAGATTGGCAG +GAATTAAACCTACGAAAATTTAGTTAACAGCTAAATACCCTATTACTGGCTTCAATCTAC +TTCTACCGCCGAAAAAAAAAAATGGCGGTAGAAGTCTTAGTAGAGATTTCTCTACACCTT +CGAATTTGCAATTCGACATGAATATCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAAC +CTCTGTGTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATTAATC +GTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCT +GAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAG +GTGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTA +TAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCAC +TAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCC +TACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAG +GATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACC +TAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTA +TTACCACTATTATCAACATGAAACCCCCAGCCATAACACAGTATCAAACTCCACTATTTG +TCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAG |
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| diff -r 32e1bfc6b7b2 -r 4ec6717872b1 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Aug 15 13:54:40 2018 -0400 +++ b/tool_data_table_conf.xml.test Fri Aug 17 08:22:49 2018 -0400 |
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| @@ -2,7 +2,7 @@ <!-- Locations of genome fasta files --> <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> </table> </tables> |