| Previous changeset 1:85c57cc9b558 (2019-12-02) Next changeset 3:0d18a3ba2d1c (2022-04-04) |
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Commit message:
"planemo upload commit 9f3f6fbbe2653d4c42818a89d6897ddaef6706b1" |
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modified:
breseq.xml macros.xml test-data/gdout.txt test-data/log.txt test-data/report.html |
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added:
test-data/lambda.short_sequence_repeats.fastq.gz |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e breseq.xml --- a/breseq.xml Mon Dec 02 04:51:27 2019 -0500 +++ b/breseq.xml Wed Apr 07 12:17:45 2021 +0000 |
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| @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="0.34.0">breseq</requirement> + <requirement type="package" version="0.35.5">breseq</requirement> <requirement type="package" version="1.32">tar</requirement> </requirements> @@ -130,7 +130,7 @@ </param> <when value="detect"> - <param name="fastqs" type="data" format="fastq" multiple="true" label="Fastq Read Files" /> + <param name="fastqs" type="data" format="fastq,fastq.gz" multiple="true" label="Fastq Read Files" /> <param argument="--polymorphism-prediction" name="polymorphism_prediction" type="select" label="Detection Mode" help="**Polymorphism mode**: Detect variants with frequencies between 0% and 100% if a mixture model is well-supported by the read alignment evidence. Use to analyze a mixed population of genomes evolved from a common ancestor. **Consensus mode**: Detect variants present in 100% of the sample. Use when re-sequencing a clonal haploid genome. This mode is the default."> <option value="" selected="true">Consensus</option> @@ -216,7 +216,7 @@ </repeat> <conditional name="run"> <param name="mode" value="detect" /> - <param name="fastqs" value="lambda.short_sequence_repeats.fastq" /> + <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz" /> <param name="polymorphism_prediction" value="" /> <param name="name" value="smallest" /> <param name="predict_junctions" value="" /> @@ -247,7 +247,7 @@ </repeat> <conditional name="run"> <param name="mode" value="detect" /> - <param name="fastqs" value="lambda.short_sequence_repeats.fastq" /> + <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz"/> <param name="polymorphism_prediction" value="" /> <param name="name" value="smallest" /> <param name="predict_junctions" value="" /> |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e macros.xml --- a/macros.xml Mon Dec 02 04:51:27 2019 -0500 +++ b/macros.xml Wed Apr 07 12:17:45 2021 +0000 |
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| @@ -1,6 +1,6 @@ <macros> - <token name="@PACKAGE_VERSION@" >0.34.0</token> - <token name="@GALAXY_VERSION@" >2</token> + <token name="@PACKAGE_VERSION@" >0.35.5</token> + <token name="@GALAXY_VERSION@" >0</token> <xml name="annotate_format_opts"> <section name="output_options" title="Output Options" expanded="false"> <param argument="--format" name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats" help="Note, this tool will run as many times (serially) as the number of output formats selected."> |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/gdout.txt --- a/test-data/gdout.txt Mon Dec 02 04:51:27 2019 -0500 +++ b/test-data/gdout.txt Wed Apr 07 12:17:45 2021 +0000 |
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| b'@@ -1,29 +1,29 @@\n #=GENOME_DIFF\t1.0\n #=TITLE\tsmallest\n-#=CREATED\t16:09:36 17 Oct 2019\n-#=PROGRAM\tbreseq 0.34.0 \n-#=COMMAND\tbreseq --num-processors 1 -o results --reference /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat --name smallest\n-#=REFSEQ\t/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat\n-#=READSEQ\t/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat\n+#=CREATED\t12:47:14 07 Apr 2021\n+#=PROGRAM\tbreseq 0.35.5 \n+#=COMMAND\tbreseq --num-processors 1 -o results --reference /home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk /tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat --name smallest\n+#=REFSEQ\t/home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk\n+#=READSEQ\t/tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat\n #=CONVERTED-BASES\t250000\n #=CONVERTED-READS\t5000\n #=INPUT-BASES\t250000\n #=INPUT-READS\t5000\n-#=MAPPED-BASES\t243031\n-#=MAPPED-READS\t4872\n+#=MAPPED-BASES\t242755\n+#=MAPPED-READS\t4870\n INS\t1\t11\tNC_001416\t41405\tGCGGCGGCG\trepeat_length=3\trepeat_new_copies=5\trepeat_ref_copies=2\trepeat_seq=GCG\n DEL\t2\t8,12\tNC_001416\t41601\t3\trepeat_length=3\trepeat_new_copies=1\trepeat_ref_copies=2\trepeat_seq=AAC\n INS\t3\t13\tNC_001416\t41716\tTTTT\trepeat_length=1\trepeat_new_copies=9\trepeat_ref_copies=5\trepeat_seq=T\n DEL\t4\t9,14\tNC_001416\t44075\t4\trepeat_length=4\trepeat_new_copies=1\trepeat_ref_copies=2\trepeat_seq=CAAA\n SNP\t5\t6\tNC_001416\t47317\tT\n-RA\t6\t.\tNC_001416\t47317\t0\tN\tT\tconsensus_score=103.5\tfrequency=1\tmajor_base=T\tmajor_cov=17/17\tmajor_frequency=1.000e+00\tminor_base=N\tminor_cov=0/0\tnew_cov=17/17\tpolymorphism_frequency=1.000e+00\tpolymorphism_score=NA\tprediction=consensus\tref_cov=0/0\ttotal_cov=17/17\n+RA\t6\t.\tNC_001416\t47317\t0\tN\tT\tconsensus_score=105.6\tfrequency=1\tmajor_base=T\tmajor_cov=17/17\tmajor_frequency=1.000e+00\tminor_base=N\tminor_cov=0/0\tnew_cov=17/17\tpolymorphism_frequency=1.000e+00\tpolymorphism_score=NA\tprediction=consensus\tref_cov=0/0\ttotal_cov=17/17\n MC\t7\t.\tNC_001416\t1\t38810\t0\t0\tleft_inside_cov=0\tleft_outside_cov=NA\tright_inside_cov=10\tright_outside_cov=13\n MC\t8\t.\tNC_001416\t41601\t41603\t0\t0\tleft_inside_cov=0\tleft_outside_cov=29\tright_inside_cov=0\tright_outside_cov=28\n MC\t9\t.\tNC_001416\t44075\t44078\t0\t0\tleft_inside_cov=0\tleft_outside_cov=28\tright_inside_cov=0\tright_outside_cov=27\n MC\t10\t.\tNC_001416\t48475\t48502\t0\t0\tleft_inside_cov=10\tleft_outside_cov=12\tright_inside_cov=0\tright_outside_cov=NA\n-JC\t11\t.\tNC_001416\t41398\t1\tNC_001416\t41405\t-1\t-1\talignment_overlap=-1\tcoverage_minus=6\tcoverage_plus=18\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=48\tkey=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0\tmax_left=44\tmax_left_minus=39\tmax_left_plus=44\tmax_min_left=24\tmax_min_left_minus=23\tmax_min_left_plus=24\tmax_min_right=23\tmax_min_right_minus=11\tmax_min_right_plus=23\tmax_pos_hash_score=96\tmax_right=47\tmax_right_minus=34\tmax_right_plus=47\tneg_log10_pos_hash_p_value=0.0\tnew_junction_coverage=1.10\tnew_junction_read_count=27\tpolymorphism_frequency=9.168e-01\tpos_hash_score=22\tprediction=consensus\tside_1_annotate_key=gene\tside_1_continuation=0\tside_1_coverage=0.04\tside_1_overlap=0\tside_1_possible_overlap_registers=49\tside_1_read_count=1\tside_1_redundant=0\tside_2_annotate_key=gene\tside_2_continuation=0\tside_2_coverage=0.16\tside_2_overlap=0\tside_2_possible_overlap_registers=49\tside_2_read_count=4\tside_2_redundant=0\ttotal_non_overlap_reads=24\tunique_read_sequence=C\n+JC\t11\t.\tNC_001416\t41398\t1\tNC_001416\t41405\t-1\t-1\talignment_overlap=-1\tcoverage_minus=5\tcoverage_plus=18\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=48\tkey=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0\tmax_left=44\tmax_left_minus=38\tmax_left_plus=44\tmax_min_left=24\tmax_min_left_minus=23\tmax_min_left_plus=24\tmax_m'..b'rage_plus=8\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=45\tkey=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0\tmax_left=42\tmax_left_minus=42\tmax_left_plus=38\tmax_min_left=22\tmax_min_left_minus=20\tmax_min_left_plus=22\tmax_min_right=20\tmax_min_right_minus=12\tmax_min_right_plus=20\tmax_pos_hash_score=90\tmax_right=44\tmax_right_minus=44\tmax_right_plus=37\tneg_log10_pos_hash_p_value=0.0\tnew_junction_coverage=1.00\tnew_junction_read_count=23\tpolymorphism_frequency=1.000e+00\tpos_hash_score=19\tprediction=consensus\tside_1_annotate_key=gene\tside_1_continuation=0\tside_1_coverage=0.00\tside_1_overlap=4\tside_1_possible_overlap_registers=49\tside_1_read_count=0\tside_1_redundant=0\tside_2_annotate_key=gene\tside_2_continuation=0\tside_2_coverage=0.00\tside_2_overlap=0\tside_2_possible_overlap_registers=45\tside_2_read_count=0\tside_2_redundant=0\ttotal_non_overlap_reads=22\n-JC\t13\t.\tNC_001416\t41711\t-1\tNC_001416\t41712\t1\t-4\talignment_overlap=-4\tcoverage_minus=10\tcoverage_plus=11\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=45\tkey=NC_001416__41711__-1__NC_001416__41712__1__-4__TTTT__50__50__0__0\tmax_left=42\tmax_left_minus=42\tmax_left_plus=30\tmax_min_left=19\tmax_min_left_minus=19\tmax_min_left_plus=19\tmax_min_right=22\tmax_min_right_minus=19\tmax_min_right_plus=22\tmax_pos_hash_score=80\tmax_right=40\tmax_right_minus=37\tmax_right_plus=40\tneg_log10_pos_hash_p_value=0.0\tnew_junction_coverage=1.30\tnew_junction_read_count=30\tpolymorphism_frequency=1.000e+00\tpos_hash_score=20\tprediction=consensus\tside_1_annotate_key=gene\tside_1_continuation=5\tside_1_coverage=0.00\tside_1_overlap=0\tside_1_possible_overlap_registers=44\tside_1_read_count=0\tside_1_redundant=0\tside_2_annotate_key=gene\tside_2_continuation=0\tside_2_coverage=0.00\tside_2_overlap=0\tside_2_possible_overlap_registers=49\tside_2_read_count=0\tside_2_redundant=0\ttotal_non_overlap_reads=21\tunique_read_sequence=TTTT\n+JC\t13\t.\tNC_001416\t41712\t1\tNC_001416\t41715\t-1\t0\talignment_overlap=1\tcoverage_minus=11\tcoverage_plus=11\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=48\tkey=NC_001416__41712__1__NC_001416__41716__-1__1____50__50__0__0\tmax_left=48\tmax_left_minus=39\tmax_left_plus=48\tmax_min_left=21\tmax_min_left_minus=21\tmax_min_left_plus=18\tmax_min_right=23\tmax_min_right_minus=23\tmax_min_right_plus=23\tmax_pos_hash_score=96\tmax_right=46\tmax_right_minus=34\tmax_right_plus=46\tneg_log10_pos_hash_p_value=0.0\tnew_junction_coverage=1.06\tnew_junction_read_count=26\tpolymorphism_frequency=8.826e-01\tpos_hash_score=21\tprediction=consensus\tside_1_annotate_key=gene\tside_1_continuation=0\tside_1_coverage=0.16\tside_1_overlap=1\tside_1_possible_overlap_registers=49\tside_1_read_count=4\tside_1_redundant=0\tside_2_annotate_key=gene\tside_2_continuation=0\tside_2_coverage=0.12\tside_2_overlap=0\tside_2_possible_overlap_registers=48\tside_2_read_count=3\tside_2_redundant=0\ttotal_non_overlap_reads=22\n JC\t14\t.\tNC_001416\t44074\t-1\tNC_001416\t44079\t1\t0\talignment_overlap=5\tcoverage_minus=19\tcoverage_plus=5\tflanking_left=50\tflanking_right=50\tfrequency=1\tjunction_possible_overlap_registers=44\tkey=NC_001416__44074__-1__NC_001416__44074__1__5____50__50__0__0\tmax_left=44\tmax_left_minus=43\tmax_left_plus=44\tmax_min_left=21\tmax_min_left_minus=21\tmax_min_left_plus=18\tmax_min_right=22\tmax_min_right_minus=22\tmax_min_right_plus=12\tmax_pos_hash_score=88\tmax_right=43\tmax_right_minus=43\tmax_right_plus=27\tneg_log10_pos_hash_p_value=0.0\tnew_junction_coverage=1.11\tnew_junction_read_count=25\tpolymorphism_frequency=1.000e+00\tpos_hash_score=20\tprediction=consensus\tside_1_annotate_key=gene\tside_1_continuation=0\tside_1_coverage=0.00\tside_1_overlap=5\tside_1_possible_overlap_registers=49\tside_1_read_count=0\tside_1_redundant=0\tside_2_annotate_key=gene\tside_2_continuation=0\tside_2_coverage=0.00\tside_2_overlap=0\tside_2_possible_overlap_registers=44\tside_2_read_count=0\tside_2_redundant=0\ttotal_non_overlap_reads=24\n UN\t15\t.\tNC_001416\t1\t38807\n UN\t16\t.\tNC_001416\t41601\t41603\n' |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/lambda.short_sequence_repeats.fastq.gz |
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| Binary file test-data/lambda.short_sequence_repeats.fastq.gz has changed |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/log.txt --- a/test-data/log.txt Mon Dec 02 04:51:27 2019 -0500 +++ b/test-data/log.txt Wed Apr 07 12:17:45 2021 +0000 |
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| @@ -1,4 +1,4 @@ -Thu Oct 17 16:09:32 2019 +Wed Apr 7 12:46:45 2021 -breseq --num-processors 1 -o results --reference /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat --name smallest +breseq --num-processors 1 -o results --reference /tmp/tmpld3eebea/files/3/b/d/dataset_3bd49447-677c-47c9-af83-1faa6f250e8b.dat /tmp/tmpld3eebea/files/e/5/8/dataset_e5864299-c116-4b7a-99b8-a39bd2f2c727.dat --name smallest |
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| diff -r 85c57cc9b558 -r 82fb5e3bb93e test-data/report.html --- a/test-data/report.html Mon Dec 02 04:51:27 2019 -0500 +++ b/test-data/report.html Wed Apr 07 12:17:45 2021 +0000 |
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| @@ -55,7 +55,7 @@ <tr> <td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td> <td width="100%"> -<b><i>breseq</i></b> version 0.34.0 +<b><i>breseq</i></b> version 0.35.5 <br><a href="index.html">mutation predictions</a> | <a href="marginal.html">marginal predictions</a> | <a href="summary.html">summary statistics</a> | |