| Previous changeset 3:a199cd7ac344 (2020-04-18) Next changeset 5:7c847ec300b8 (2021-09-12) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150" |
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modified:
macros.xml racon.xml |
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| diff -r a199cd7ac344 -r cd06929b224b macros.xml --- a/macros.xml Sat Apr 18 19:39:13 2020 -0400 +++ b/macros.xml Sun Aug 29 10:49:02 2021 +0000 |
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| @@ -1,11 +1,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">racon</requirement> + <requirement type="package" version="@TOOL_VERSION@">racon</requirement> <yield/> </requirements> </xml> - <token name="@VERSION@">1.4.13</token> + <token name="@TOOL_VERSION@">1.4.13</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.214270.116</citation> |
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| diff -r a199cd7ac344 -r cd06929b224b racon.xml --- a/racon.xml Sat Apr 18 19:39:13 2020 -0400 +++ b/racon.xml Sun Aug 29 10:49:02 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="racon" name="Racon" version="@VERSION@"> +<tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> <macros> <import>macros.xml</import> @@ -6,22 +6,40 @@ <expand macro="requirements" /> <version_command>racon --version</version_command> <command detect_errors="exit_code"><![CDATA[ - ln -s '$reads' reads.${reads.ext} && + #if $reads.ext.startswith("fasta") + #set ext="fasta" + #else + #set ext="fastq" + #end if + #if $reads.ext.endswith(".gz") + #set ext=ext+".gz" + #end if + + ln -s '$reads' reads.$ext && #if $overlaps.ext == 'sam': ln -s '$overlaps' overlaps.${overlaps.ext} && #else: ln -s '$overlaps' overlaps.paf && #end if - ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && + + #if $corrected_reads.ext.startswith("fasta") + #set cext="fasta" + #else + #set cext="fastq" + #end if + #if $corrected_reads.ext.endswith(".gz") + #set cext=cext+".gz" + #end if + ln -s '$corrected_reads' corrected_reads.$cext && racon - reads.${reads.ext} + reads.$ext #if $overlaps.ext == 'sam': overlaps.${overlaps.ext} #else: overlaps.paf #end if - corrected_reads.${corrected_reads.ext} + corrected_reads.$cext -t \${GALAXY_SLOTS:-4} $u $f |