| Previous changeset 0:3cde72a6e37c (2020-05-23) Next changeset 2:d50c1d5b72ce (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 tool_data_table_conf.xml.sample variant.xml |
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added:
test-data/variants.vcf.gz |
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| diff -r 3cde72a6e37c -r 43388fc8ad0b macros.xml --- a/macros.xml Sat May 23 13:36:47 2020 -0400 +++ b/macros.xml Thu May 28 02:38:34 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 3cde72a6e37c -r 43388fc8ad0b test-data/variants.vcf.gz |
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| Binary file test-data/variants.vcf.gz has changed |
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| diff -r 3cde72a6e37c -r 43388fc8ad0b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat May 23 13:36:47 2020 -0400 +++ b/tool_data_table_conf.xml.sample Thu May 28 02:38:34 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> |
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| diff -r 3cde72a6e37c -r 43388fc8ad0b variant.xml --- a/variant.xml Sat May 23 13:36:47 2020 -0400 +++ b/variant.xml Thu May 28 02:38:34 2020 -0400 |
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| @@ -7,26 +7,26 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ - ## initialize - @REF_FASTA@ +## initialize +@REF_FASTA@ - ## run - medaka variant - ## optional - --debug - #if $region - --region '${region}' - #end if - $verbose - ## required - 'reference.fa' - #for $current in $inputs - '$current' - #end for - 'result.vcf' ## output +## run +medaka variant +## optional +--debug +#if $region + --region '${region}' +#end if +$verbose +## required +reference.fa +#for $current in $inputs + '$current' +#end for +'$out_result' ## output - |& tee log.txt - ]]></command> +|& tee '$out_log' + ]]></command> <inputs> <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/> <expand macro="reference"/> @@ -39,11 +39,11 @@ </inputs> <outputs> <!-- standard --> - <data name="out_result" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result"> + <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"> <filter>'result' in out</filter> </data> <!-- optional --> - <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log"> + <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log"> <filter>'log' in out</filter> </data> </outputs> |