| Previous changeset 2:ee0d6e789958 (2024-01-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 8e54473840ee1238da9cb8a77cf136f00b40e4e7 |
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modified:
hapog.xml test-data/hapog_bam.changes test-data/hapog_bam.fasta |
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| diff -r ee0d6e789958 -r 5287036a797a hapog.xml --- a/hapog.xml Sun Jan 28 23:46:07 2024 +0000 +++ b/hapog.xml Fri Apr 05 09:39:36 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>genome polishing</description> <macros> - <token name="@TOOL_VERSION@">1.3.7</token> + <token name="@TOOL_VERSION@">1.3.8</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <xrefs> @@ -65,7 +65,7 @@ <param name="bam" type="data" format="bam" label="Pre-aligned reads"/> </when> </conditional> - <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" /> + <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output"/> </inputs> <outputs> <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/> @@ -73,51 +73,51 @@ </outputs> <tests> <test> - <param name="genome" value="genome.fa" /> + <param name="genome" value="genome.fa"/> <conditional name="reads"> - <param name="type" value="short" /> - <param name="pe1" value="fastq1.fq" /> - <param name="pe2" value="fastq2.fq" /> + <param name="type" value="short"/> + <param name="pe1" value="fastq1.fq"/> + <param name="pe2" value="fastq2.fq"/> </conditional> - <output name="output" file="hapog_short.fasta" /> - <output name="changes" file="hapog_short.changes" /> + <output name="output" file="hapog_short.fasta"/> + <output name="changes" file="hapog_short.changes"/> </test> <test> - <param name="genome" value="genome.fa" /> + <param name="genome" value="genome.fa"/> <conditional name="reads"> - <param name="type" value="short" /> - <param name="pe1" value="fastq1.fq.gz" /> - <param name="pe2" value="fastq2.fq.gz" /> + <param name="type" value="short"/> + <param name="pe1" value="fastq1.fq.gz"/> + <param name="pe2" value="fastq2.fq.gz"/> </conditional> <output name="output" file="hapog_short.fasta"/> - <output name="changes" file="hapog_short.changes" /> + <output name="changes" file="hapog_short.changes"/> </test> <test> - <param name="genome" value="genome.fa" /> + <param name="genome" value="genome.fa"/> <conditional name="reads"> - <param name="type" value="long" /> - <param name="single" value="fastq1.fq" /> + <param name="type" value="long"/> + <param name="single" value="fastq1.fq"/> </conditional> - <output name="output" file="hapog_long.fasta" /> - <output name="changes" file="hapog_long.changes" /> + <output name="output" file="hapog_long.fasta"/> + <output name="changes" file="hapog_long.changes"/> </test> <test> - <param name="genome" value="genome.fa" /> + <param name="genome" value="genome.fa"/> <conditional name="reads"> - <param name="type" value="long" /> - <param name="single" value="fastq1.fq.gz" /> + <param name="type" value="long"/> + <param name="single" value="fastq1.fq.gz"/> </conditional> <output name="output" file="hapog_long.fasta"/> - <output name="changes" file="hapog_long.changes" /> + <output name="changes" file="hapog_long.changes"/> </test> <test> - <param name="genome" value="genome.fa" /> + <param name="genome" value="genome.fa"/> <conditional name="reads"> - <param name="type" value="bam" /> - <param name="bam" value="input.bam" /> + <param name="type" value="bam"/> + <param name="bam" value="input.bam"/> </conditional> <output name="output" file="hapog_bam.fasta"/> - <output name="changes" file="hapog_bam.changes" /> + <output name="changes" file="hapog_bam.changes"/> </test> </tests> <help><![CDATA[ |
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| diff -r ee0d6e789958 -r 5287036a797a test-data/hapog_bam.changes --- a/test-data/hapog_bam.changes Sun Jan 28 23:46:07 2024 +0000 +++ b/test-data/hapog_bam.changes Fri Apr 05 09:39:36 2024 +0000 |
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| @@ -1,3 +1,2 @@ NC_0129201 72 ref=A read=G readname=M01368:8:000000000-A3GHV:1:1101:6911:8255 homo ratio1=1.0000 ratio2=1.0000 -NC_0129201 16525 ref=G read=A readname=M01368:8:000000000-A3GHV:1:1104:11928:24197 homo ratio1=0.9752 ratio2=0.9752 |
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| diff -r ee0d6e789958 -r 5287036a797a test-data/hapog_bam.fasta --- a/test-data/hapog_bam.fasta Sun Jan 28 23:46:07 2024 +0000 +++ b/test-data/hapog_bam.fasta Fri Apr 05 09:39:36 2024 +0000 |
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| @@ -274,6 +274,6 @@ CATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCT ACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT -CTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGAC +CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGAC ATCACGATG |