| Previous changeset 12:478f36effca1 (2018-10-17) Next changeset 14:983552d5822d (2019-11-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d" |
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modified:
align_and_estimate_abundance.xml macros.xml test-data/count/contig_exn50_statistic/ExN50.stats test-data/supertranscripts/trinity_genes.fasta test-data/supertranscripts/trinity_genes.gtf |
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| diff -r 478f36effca1 -r 6d6b72d14170 align_and_estimate_abundance.xml --- a/align_and_estimate_abundance.xml Wed Oct 17 12:57:01 2018 -0400 +++ b/align_and_estimate_abundance.xml Fri Nov 01 08:09:49 2019 -0400 |
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| @@ -4,9 +4,8 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="1.3.0">rsem</requirement> - <requirement type="package" version="1.5.1">express</requirement> - <requirement type="package" version="0.43.1">kallisto</requirement> + <requirement type="package" version="1.3.2">rsem</requirement> + <requirement type="package" version="0.46.0">kallisto</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ ln -f -s '$transcripts' input.fa && @@ -40,7 +39,7 @@ --transcripts input.fa --est_method $method.est_method - #if $method.est_method == "RSEM" or $method.est_method == "eXpress": + #if $method.est_method == "RSEM": --aln_method $method.aln_method #else if $method.est_method == "salmon": --salmon_idx_type $method.salmon_idx_type @@ -124,7 +123,6 @@ <conditional name="method"> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> - <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> <option value="kallisto">Kallisto</option> </param> @@ -134,12 +132,6 @@ <option value="bowtie2">Bowtie2</option> </param> </when> - <when value="eXpress"> - <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> - <option value="bowtie">Bowtie</option> - <option value="bowtie2">Bowtie2</option> - </param> - </when> <when value="salmon"> <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> <option value="quasi">Quasi</option> @@ -173,12 +165,6 @@ <filter>method['est_method'] == "RSEM"</filter> </data> - <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs"> - <filter>method['est_method'] == "eXpress"</filter> - </data> - <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes"> - <filter>method['est_method'] == "eXpress"</filter> - </data> <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> <filter>method['est_method'] == "salmon"</filter> @@ -248,29 +234,6 @@ <param name="transcripts" value="raw/Trinity.fasta"/> <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/> - <param name="est_method" value="eXpress"/> - <param name="aln_method" value="bowtie"/> - <param name="has_gene_map" value="yes"/> - <output name="isoforms_counts_express"> - <assert_contents> - <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> - <has_n_columns n="15" /> - </assert_contents> - </output> - <output name="genes_counts_express"> - <assert_contents> - <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> - <has_n_columns n="15" /> - </assert_contents> - </output> - </test> - <test> - <param name="paired_or_single" value="paired"/> - <param name="left_input" value="reads.left.fq"/> - <param name="right_input" value="reads.right.fq"/> - <param name="transcripts" value="raw/Trinity.fasta"/> - <param name="gene_to_trans" value="raw/Trinity.map" /> - <param name="library_type" value="RF"/> <param name="est_method" value="salmon"/> <param name="aln_method" value="bowtie"/> <param name="has_gene_map" value="yes"/> |
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| diff -r 478f36effca1 -r 6d6b72d14170 macros.xml --- a/macros.xml Wed Oct 17 12:57:01 2018 -0400 +++ b/macros.xml Fri Nov 01 08:09:49 2019 -0400 |
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| @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.8.4</token> + <token name="@WRAPPER_VERSION@">2.8.5</token> <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> #if $pool.inputs.strand.is_strand_specific: |
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| diff -r 478f36effca1 -r 6d6b72d14170 test-data/count/contig_exn50_statistic/ExN50.stats --- a/test-data/count/contig_exn50_statistic/ExN50.stats Wed Oct 17 12:57:01 2018 -0400 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Fri Nov 01 08:09:49 2019 -0400 |
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| @@ -1,4 +1,5 @@ Ex ExN50 num_transcripts 33 541 1 67 541 2 +99 380 3 100 279 7 |
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| diff -r 478f36effca1 -r 6d6b72d14170 test-data/supertranscripts/trinity_genes.fasta --- a/test-data/supertranscripts/trinity_genes.fasta Wed Oct 17 12:57:01 2018 -0400 +++ b/test-data/supertranscripts/trinity_genes.fasta Fri Nov 01 08:09:49 2019 -0400 |
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| @@ -1,14 +1,14 @@ ->TRINITY_DN1_c0_g1 -CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN2_c3_g1 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA >TRINITY_DN0_c0_g1 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC >TRINITY_DN2_c0_g1 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ->TRINITY_DN2_c1_g1 -GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN3_c0_g1 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT >TRINITY_DN2_c2_g1 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC ->TRINITY_DN2_c3_g1 -GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1 -ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +>TRINITY_DN2_c1_g1 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN1_c0_g1 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG |
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| diff -r 478f36effca1 -r 6d6b72d14170 test-data/supertranscripts/trinity_genes.gtf --- a/test-data/supertranscripts/trinity_genes.gtf Wed Oct 17 12:57:01 2018 -0400 +++ b/test-data/supertranscripts/trinity_genes.gtf Fri Nov 01 08:09:49 2019 -0400 |
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| @@ -1,14 +1,14 @@ -TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" +TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" TRINITY_DN0_c0_g1 Trinity_gene exon 1 229 . + . gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1" TRINITY_DN2_c0_g1 Trinity_gene exon 1 279 . + . gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1" -TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" +TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" TRINITY_DN2_c2_g1 Trinity_gene exon 1 240 . + . gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1" -TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" +TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" -TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" +TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" |