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changeset 2:82fb5e3bb93e draft

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"planemo upload commit 9f3f6fbbe2653d4c42818a89d6897ddaef6706b1"
author iuc
date Wed, 07 Apr 2021 12:17:45 +0000
parents 85c57cc9b558
children 0d18a3ba2d1c
files breseq.xml macros.xml test-data/gdout.txt test-data/lambda.short_sequence_repeats.fastq.gz test-data/log.txt test-data/report.html
diffstat 6 files changed, 19 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/breseq.xml	Mon Dec 02 04:51:27 2019 -0500
+++ b/breseq.xml	Wed Apr 07 12:17:45 2021 +0000
@@ -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="" />
--- a/macros.xml	Mon Dec 02 04:51:27 2019 -0500
+++ b/macros.xml	Wed Apr 07 12:17:45 2021 +0000
@@ -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.">
--- 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
@@ -1,29 +1,29 @@
 #=GENOME_DIFF	1.0
 #=TITLE	smallest
-#=CREATED	16:09:36 17 Oct 2019
-#=PROGRAM	breseq 0.34.0 
-#=COMMAND	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
-#=REFSEQ	/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat
-#=READSEQ	/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat
+#=CREATED	12:47:14 07 Apr 2021
+#=PROGRAM	breseq 0.35.5 
+#=COMMAND	breseq --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
+#=REFSEQ	/home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk
+#=READSEQ	/tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat
 #=CONVERTED-BASES	250000
 #=CONVERTED-READS	5000
 #=INPUT-BASES	250000
 #=INPUT-READS	5000
-#=MAPPED-BASES	243031
-#=MAPPED-READS	4872
+#=MAPPED-BASES	242755
+#=MAPPED-READS	4870
 INS	1	11	NC_001416	41405	GCGGCGGCG	repeat_length=3	repeat_new_copies=5	repeat_ref_copies=2	repeat_seq=GCG
 DEL	2	8,12	NC_001416	41601	3	repeat_length=3	repeat_new_copies=1	repeat_ref_copies=2	repeat_seq=AAC
 INS	3	13	NC_001416	41716	TTTT	repeat_length=1	repeat_new_copies=9	repeat_ref_copies=5	repeat_seq=T
 DEL	4	9,14	NC_001416	44075	4	repeat_length=4	repeat_new_copies=1	repeat_ref_copies=2	repeat_seq=CAAA
 SNP	5	6	NC_001416	47317	T
-RA	6	.	NC_001416	47317	0	N	T	consensus_score=103.5	frequency=1	major_base=T	major_cov=17/17	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/17	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/17
+RA	6	.	NC_001416	47317	0	N	T	consensus_score=105.6	frequency=1	major_base=T	major_cov=17/17	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/17	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/17
 MC	7	.	NC_001416	1	38810	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=10	right_outside_cov=13
 MC	8	.	NC_001416	41601	41603	0	0	left_inside_cov=0	left_outside_cov=29	right_inside_cov=0	right_outside_cov=28
 MC	9	.	NC_001416	44075	44078	0	0	left_inside_cov=0	left_outside_cov=28	right_inside_cov=0	right_outside_cov=27
 MC	10	.	NC_001416	48475	48502	0	0	left_inside_cov=10	left_outside_cov=12	right_inside_cov=0	right_outside_cov=NA
-JC	11	.	NC_001416	41398	1	NC_001416	41405	-1	-1	alignment_overlap=-1	coverage_minus=6	coverage_plus=18	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0	max_left=44	max_left_minus=39	max_left_plus=44	max_min_left=24	max_min_left_minus=23	max_min_left_plus=24	max_min_right=23	max_min_right_minus=11	max_min_right_plus=23	max_pos_hash_score=96	max_right=47	max_right_minus=34	max_right_plus=47	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.10	new_junction_read_count=27	polymorphism_frequency=9.168e-01	pos_hash_score=22	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=49	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=24	unique_read_sequence=C
+JC	11	.	NC_001416	41398	1	NC_001416	41405	-1	-1	alignment_overlap=-1	coverage_minus=5	coverage_plus=18	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0	max_left=44	max_left_minus=38	max_left_plus=44	max_min_left=24	max_min_left_minus=23	max_min_left_plus=24	max_min_right=23	max_min_right_minus=11	max_min_right_plus=23	max_pos_hash_score=96	max_right=47	max_right_minus=34	max_right_plus=47	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.10	new_junction_read_count=27	polymorphism_frequency=9.168e-01	pos_hash_score=21	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=49	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=23	unique_read_sequence=C
 JC	12	.	NC_001416	41600	-1	NC_001416	41604	1	0	alignment_overlap=4	coverage_minus=14	coverage_plus=8	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=45	key=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0	max_left=42	max_left_minus=42	max_left_plus=38	max_min_left=22	max_min_left_minus=20	max_min_left_plus=22	max_min_right=20	max_min_right_minus=12	max_min_right_plus=20	max_pos_hash_score=90	max_right=44	max_right_minus=44	max_right_plus=37	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.00	new_junction_read_count=23	polymorphism_frequency=1.000e+00	pos_hash_score=19	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=49	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=45	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=22
-JC	13	.	NC_001416	41711	-1	NC_001416	41712	1	-4	alignment_overlap=-4	coverage_minus=10	coverage_plus=11	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=45	key=NC_001416__41711__-1__NC_001416__41712__1__-4__TTTT__50__50__0__0	max_left=42	max_left_minus=42	max_left_plus=30	max_min_left=19	max_min_left_minus=19	max_min_left_plus=19	max_min_right=22	max_min_right_minus=19	max_min_right_plus=22	max_pos_hash_score=80	max_right=40	max_right_minus=37	max_right_plus=40	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.30	new_junction_read_count=30	polymorphism_frequency=1.000e+00	pos_hash_score=20	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=5	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=44	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=49	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=21	unique_read_sequence=TTTT
+JC	13	.	NC_001416	41712	1	NC_001416	41715	-1	0	alignment_overlap=1	coverage_minus=11	coverage_plus=11	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=48	key=NC_001416__41712__1__NC_001416__41716__-1__1____50__50__0__0	max_left=48	max_left_minus=39	max_left_plus=48	max_min_left=21	max_min_left_minus=21	max_min_left_plus=18	max_min_right=23	max_min_right_minus=23	max_min_right_plus=23	max_pos_hash_score=96	max_right=46	max_right_minus=34	max_right_plus=46	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.06	new_junction_read_count=26	polymorphism_frequency=8.826e-01	pos_hash_score=21	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.16	side_1_overlap=1	side_1_possible_overlap_registers=49	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.12	side_2_overlap=0	side_2_possible_overlap_registers=48	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=22
 JC	14	.	NC_001416	44074	-1	NC_001416	44079	1	0	alignment_overlap=5	coverage_minus=19	coverage_plus=5	flanking_left=50	flanking_right=50	frequency=1	junction_possible_overlap_registers=44	key=NC_001416__44074__-1__NC_001416__44074__1__5____50__50__0__0	max_left=44	max_left_minus=43	max_left_plus=44	max_min_left=21	max_min_left_minus=21	max_min_left_plus=18	max_min_right=22	max_min_right_minus=22	max_min_right_plus=12	max_pos_hash_score=88	max_right=43	max_right_minus=43	max_right_plus=27	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.11	new_junction_read_count=25	polymorphism_frequency=1.000e+00	pos_hash_score=20	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=5	side_1_possible_overlap_registers=49	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=44	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=24
 UN	15	.	NC_001416	1	38807
 UN	16	.	NC_001416	41601	41603
Binary file test-data/lambda.short_sequence_repeats.fastq.gz has changed
--- 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
@@ -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
 
--- 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
@@ -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>&nbsp;&nbsp;version 0.34.0&nbsp;&nbsp;
+<b><i>breseq</i></b>&nbsp;&nbsp;version 0.35.5&nbsp;&nbsp;
 <br><a href="index.html">mutation predictions</a> | 
 <a href="marginal.html">marginal predictions</a> | 
 <a href="summary.html">summary statistics</a> |