| Previous changeset 0:ef94bace3a3c (2020-05-23) Next changeset 2:6a87478ed985 (2020-06-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c" |
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modified:
macros.xml medaka_consensus.xml tool_data_table_conf.xml.sample |
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added:
test-data/variants.vcf.gz |
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| diff -r ef94bace3a3c -r 551f8c9bc4cf macros.xml --- a/macros.xml Sat May 23 13:38:26 2020 -0400 +++ b/macros.xml Thu May 28 02:39:35 2020 -0400 |
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| @@ -22,20 +22,20 @@ </citations> </xml> - <!-- + <!-- command --> - <token name="@REF_FASTA@"><![CDATA[ + <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' 'reference.fa' && + ln -f -s '$reference_source.ref_file' reference.fa && #else: - ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' && + ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if ]]></token> <!-- - input + input --> <xml name="b" token_argument="-b"> |
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| diff -r ef94bace3a3c -r 551f8c9bc4cf medaka_consensus.xml --- a/medaka_consensus.xml Sat May 23 13:38:26 2020 -0400 +++ b/medaka_consensus.xml Thu May 28 02:39:35 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>Assembly polishing via neural networks</description> <macros> <import>macros.xml</import> @@ -6,23 +6,20 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ - medaka_consensus - ## optional - -m '${m}' - -b $b - -o 'results' - #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',') - -v - #end if - -t \${GALAXY_SLOTS:-4} - ## required - -i '$i' - -d '$d' +medaka_consensus +## optional +-m ${m} +-b $b +-o results +#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',') + -v +#end if +-t \${GALAXY_SLOTS:-4} +## required +-i '$i' +-d '$d' - |& tee 'log.txt' - #if 'variants' in str($out).split(',') - && bgzip -d 'results/variants.vcf.gz' - #end if +|& tee '$out_log' ]]></command> <inputs> <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> @@ -54,14 +51,14 @@ <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus"> <filter>'draft' in out</filter> </data> - <data name="out_variants" format="vcf" from_work_dir="results/variants.vcf" label="${tool.name} on ${on_string}: Variants"> + <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants"> <filter>'variants' in out</filter> </data> <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft"> <filter>'polished' in out</filter> </data> <!-- optional --> - <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"> + <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> <filter>'log' in out</filter> </data> </outputs> @@ -124,13 +121,7 @@ <has_size value="9"/> </assert_contents> </output> - <output name="out_variants"> - <assert_contents> - <has_n_lines n="9"/> - <has_line line="##fileformat=VCFv4.1"/> - <has_text_matching expression="4	.+"/> - </assert_contents> - </output> + <output name="out_variants" file="variants.vcf.gz" decompress="true"/> <output name="out_log"> <assert_contents> <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> |
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| diff -r ef94bace3a3c -r 551f8c9bc4cf test-data/variants.vcf.gz |
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| Binary file test-data/variants.vcf.gz has changed |
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| diff -r ef94bace3a3c -r 551f8c9bc4cf tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat May 23 13:38:26 2020 -0400 +++ b/tool_data_table_conf.xml.sample Thu May 28 02:39:35 2020 -0400 |
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| @@ -4,4 +4,4 @@ <columns>value, dbkey, name, path</columns> <file path="all_fasta.loc" /> </table> -</tables> \ No newline at end of file +</tables> |