| Previous changeset 0:711d4deb7bdf (2020-05-23) Next changeset 2:ce2bf68a260d (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_variant.xml tool_data_table_conf.xml.sample |
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added:
test-data/variants.vcf.gz |
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| diff -r 711d4deb7bdf -r 92cdc29a8620 macros.xml --- a/macros.xml Sat May 23 13:37:48 2020 -0400 +++ b/macros.xml Thu May 28 02:39:16 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 '$reference_source.ref_file.fields.path' reference.fa && #end if ]]></token> <!-- - input + input --> <xml name="b" token_argument="-b"> |
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| diff -r 711d4deb7bdf -r 92cdc29a8620 medaka_variant.xml --- a/medaka_variant.xml Sat May 23 13:37:48 2020 -0400 +++ b/medaka_variant.xml Thu May 28 02:39:16 2020 -0400 |
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| @@ -6,32 +6,32 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ - ## initialize - @REF_FASTA@ - ## link doesn't work - cp '${i}' 'alignment.bam' && - cp '${i.metadata.bam_index}' 'alignment.bam.bai' && +## initialize +@REF_FASTA@ +## link doesn't work +cp '${i}' alignment.bam && +cp '${i.metadata.bam_index}' alignment.bam.bai && - ## run - medaka_variant - ## optional - #if str($r) != '' - -r '$r' - #end if - -o 'results' - -s '$s' - -m '$m' - -t \${GALAXY_SLOTS:-4} - -b $b - -N $N - -P $P - $U - $S - ## required - -i 'alignment.bam' - -f 'reference.fa' +## run +medaka_variant +## optional +#if $r: + -r '$r' +#end if +-o results +-s $s +-m $m +-t \${GALAXY_SLOTS:-4} +-b $b +-N $N +-P $P +$U +$S +## required +-i alignment.bam +-f reference.fa - |& tee 'log.txt' +|& tee '$out_log' ]]></command> <inputs> <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/> @@ -92,7 +92,7 @@ <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf"> <filter>'round_1_unfiltered_vcf' in out</filter> </data> - <data name="out_log" format="txt" label="${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> |
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| diff -r 711d4deb7bdf -r 92cdc29a8620 test-data/variants.vcf.gz |
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| Binary file test-data/variants.vcf.gz has changed |
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| diff -r 711d4deb7bdf -r 92cdc29a8620 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat May 23 13:37:48 2020 -0400 +++ b/tool_data_table_conf.xml.sample Thu May 28 02:39:16 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> |