Mercurial > repos > bgruening > racon
comparison racon.xml @ 4:cd06929b224b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
| author | bgruening |
|---|---|
| date | Sun, 29 Aug 2021 10:49:02 +0000 |
| parents | a199cd7ac344 |
| children | d865b62f501c |
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| 3:a199cd7ac344 | 4:cd06929b224b |
|---|---|
| 1 <tool id="racon" name="Racon" version="@VERSION@"> | 1 <tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> | 2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <version_command>racon --version</version_command> | 7 <version_command>racon --version</version_command> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 ln -s '$reads' reads.${reads.ext} && | 9 #if $reads.ext.startswith("fasta") |
| 10 #set ext="fasta" | |
| 11 #else | |
| 12 #set ext="fastq" | |
| 13 #end if | |
| 14 #if $reads.ext.endswith(".gz") | |
| 15 #set ext=ext+".gz" | |
| 16 #end if | |
| 17 | |
| 18 ln -s '$reads' reads.$ext && | |
| 10 #if $overlaps.ext == 'sam': | 19 #if $overlaps.ext == 'sam': |
| 11 ln -s '$overlaps' overlaps.${overlaps.ext} && | 20 ln -s '$overlaps' overlaps.${overlaps.ext} && |
| 12 #else: | 21 #else: |
| 13 ln -s '$overlaps' overlaps.paf && | 22 ln -s '$overlaps' overlaps.paf && |
| 14 #end if | 23 #end if |
| 15 ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && | 24 |
| 25 #if $corrected_reads.ext.startswith("fasta") | |
| 26 #set cext="fasta" | |
| 27 #else | |
| 28 #set cext="fastq" | |
| 29 #end if | |
| 30 #if $corrected_reads.ext.endswith(".gz") | |
| 31 #set cext=cext+".gz" | |
| 32 #end if | |
| 33 ln -s '$corrected_reads' corrected_reads.$cext && | |
| 16 | 34 |
| 17 racon | 35 racon |
| 18 reads.${reads.ext} | 36 reads.$ext |
| 19 #if $overlaps.ext == 'sam': | 37 #if $overlaps.ext == 'sam': |
| 20 overlaps.${overlaps.ext} | 38 overlaps.${overlaps.ext} |
| 21 #else: | 39 #else: |
| 22 overlaps.paf | 40 overlaps.paf |
| 23 #end if | 41 #end if |
| 24 corrected_reads.${corrected_reads.ext} | 42 corrected_reads.$cext |
| 25 -t \${GALAXY_SLOTS:-4} | 43 -t \${GALAXY_SLOTS:-4} |
| 26 $u | 44 $u |
| 27 $f | 45 $f |
| 28 -w $w | 46 -w $w |
| 29 -q $q | 47 -q $q |