| Previous changeset 3:dbd9f2db9ed8 (2020-05-29) Next changeset 5:aa35ee7f3ab2 (2020-10-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528" |
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modified:
lofreq_viterbi.xml macros.xml test-data/call-out1.vcf test-data/call-out2.vcf test-data/indel-call-out.vcf |
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| diff -r dbd9f2db9ed8 -r af7e416d8176 lofreq_viterbi.xml --- a/lofreq_viterbi.xml Fri May 29 15:24:28 2020 -0400 +++ b/lofreq_viterbi.xml Mon Jun 15 13:13:50 2020 -0400 |
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| @@ -1,28 +1,26 @@ -<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy1"> +<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy0"> <description>with LoFreq viterbi</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="1.9">samtools</requirement> - </expand> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @PREPARE_REF@ lofreq viterbi --ref '$reference_fasta_fn' - ${adv_options.delflags} + ${adv_options.keepflags} --defqual ${adv_options.bq2_handling.defqual} --out tmp.bam '$reads' && - samtools sort -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam + samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam ]]></command> <inputs> <param name="reads" type="data" format="bam" label="Reads to realign" /> <expand macro="reference_interface" /> <section name="adv_options" title="Advanced options" expanded="false"> - <param argument="--keepflags" name="delflags" type="boolean" truevalue="" falsevalue="--keepflags" checked="true" - label="Delete flags MC, MD, NM, and A?" - help="These flags are all prone to getting invalidated during realignment. Keep them only if you know what you are doing." /> + <param argument="--keepflags" type="boolean" truevalue="--keepflags" falsevalue="" checked="false" + label="Keep MC, MD, NM, and A flags?" + help="Re-alignment resets the MC, MD, NM, and A flags by default. The values of these tags depend on the exact alignment. Use this option only if you know what you are doing." /> <conditional name="bq2_handling"> <param name="replace_bq2" type="select" label="How to handle base qualities of 2?" @@ -51,17 +49,18 @@ <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> <param name="ref_selector" value="history" /> + <param name="ref_selector" value="history" /> <param name="ref" ftype="fasta" value="pBR322.fa" /> - <output name="realigned" file="viterbi-out1.bam" /> + <output name="realigned" file="viterbi-out1.bam" ftype="bam" /> </test> <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> <param name="ref_selector" value="history" /> <section name="adv_options"> - <param name="delflags" value="false" /> + <param name="keepflags" value="true" /> </section> <param name="ref" ftype="fasta" value="pBR322.fa" /> - <output name="realigned" file="viterbi-out2.bam" /> + <output name="realigned" file="viterbi-out2.bam" ftype="bam" /> </test> </tests> <help><![CDATA[ |
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| diff -r dbd9f2db9ed8 -r af7e416d8176 macros.xml --- a/macros.xml Fri May 29 15:24:28 2020 -0400 +++ b/macros.xml Mon Jun 15 13:13:50 2020 -0400 |
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| @@ -1,11 +1,11 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> - <token name="@TOOL_VERSION@">2.1.4</token> + <token name="@TOOL_VERSION@">2.1.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement> <yield/> </requirements> + <version_command>lofreq version | grep version | cut -d ' ' -f 2</version_command> </xml> <xml name="citations"> <citations> |
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| diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/call-out1.vcf --- a/test-data/call-out1.vcf Fri May 29 15:24:28 2020 -0400 +++ b/test-data/call-out1.vcf Mon Jun 15 13:13:50 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20200529 -##source=lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelqgn6kxdr/0.vcf.gz reads.bam +##fileDate=20200615 +##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> |
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| diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/call-out2.vcf --- a/test-data/call-out2.vcf Fri May 29 15:24:28 2020 -0400 +++ b/test-data/call-out2.vcf Mon Jun 15 13:13:50 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20200529 -##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelkzkzyltj/0.vcf.gz reads.bam +##fileDate=20200615 +##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallelg3dmyvln/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> |
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| diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/indel-call-out.vcf --- a/test-data/indel-call-out.vcf Fri May 29 15:24:28 2020 -0400 +++ b/test-data/indel-call-out.vcf Mon Jun 15 13:13:50 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.0 -##fileDate=20200529 -##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelafbznae0/0.vcf.gz reads.bam +##fileDate=20200615 +##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/31/working/pp-tmp/lofreq2_call_parallel4gfado3q/0.vcf.gz reads.bam ##reference=reference.fa ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> @@ -10,12 +10,12 @@ ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> #CHROM POS ID REF ALT QUAL FILTER INFO -pBR322 725 . G GN 0 . ;HRUN=1 -pBR322 746 . A AN 0 . ;HRUN=1 -pBR322 747 . T TN 0 . ;HRUN=1 -pBR322 751 . G GN 0 . ;HRUN=1 -pBR322 807 . T TN 0 . ;HRUN=3 -pBR322 943 . C CCG 0 . ;HRUN=1 -pBR322 1152 . C CN 0 . ;HRUN=2 -pBR322 1271 . A AN 0 . ;HRUN=2 -pBR322 1376 . A ANN 0 . ;HRUN=1 +pBR322 725 . G GN 0 . DP=46;AF=0.021739;SB=0;DP4=22,23,0,1;INDEL;HRUN=1 +pBR322 746 . A AN 0 . DP=225;AF=0.004444;SB=3;DP4=116,108,0,1;INDEL;HRUN=1 +pBR322 747 . T TN 0 . DP=230;AF=0.004348;SB=3;DP4=118,111,0,1;INDEL;HRUN=1 +pBR322 751 . G GN 0 . DP=255;AF=0.003922;SB=3;DP4=128,126,0,1;INDEL;HRUN=1 +pBR322 807 . T TN 0 . DP=606;AF=0.001650;SB=0;DP4=300,305,0,1;INDEL;HRUN=3 +pBR322 943 . C CCG 0 . DP=1465;AF=0.000683;SB=0;DP4=709,755,0,1;INDEL;HRUN=1 +pBR322 1152 . C CN 0 . DP=1754;AF=0.000570;SB=0;DP4=926,830,1,0;INDEL;HRUN=2 +pBR322 1271 . A AN 0 . DP=1743;AF=0.000574;SB=0;DP4=890,855,1,0;INDEL;HRUN=2 +pBR322 1376 . A ANN 0 . DP=1691;AF=0.000591;SB=3;DP4=849,843,0,1;INDEL;HRUN=1 |