| Previous changeset 11:bdfbaf0c10aa (2023-05-08) Next changeset 13:9eeb13a92d79 (2023-07-05) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cb75f42cdcae1a92023e6e5b33a8a260877d76fe |
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modified:
cactus_cactus.xml macros.xml |
| b |
| diff -r bdfbaf0c10aa -r 2263989660f5 cactus_cactus.xml --- a/cactus_cactus.xml Mon May 08 04:38:48 2023 +0000 +++ b/cactus_cactus.xml Mon May 15 04:34:02 2023 +0000 |
| [ |
| @@ -23,52 +23,16 @@ ## Run cactus #if $aln_mode.aln_mode_select == 'intraspecies': - ## If we're doing a pangenome, we need to run the steps manually - cactus-minigraph - --binariesMode local - --mapCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M - --reference $aln_mode.ref_level - --workDir ./ - ./jobStore - ./seqfile.txt - pangenome.gfa - && - cactus-graphmap + ## Run cactus-pangenome + cactus-pangenome --binariesMode local --maxCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M - --outputFasta pangenome.gfa.fa - --reference $aln_mode.ref_level - --workDir ./ - ./jobStore - ./seqfile.txt - pangenome.gfa - pangenome.paf - && - cactus-align - --binariesMode local - --maxCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M - --outVG - --pangenome - --reference $aln_mode.ref_level - --workDir ./ - ./jobStore - ./seqfile.txt - pangenome.paf - alignment.hal - && - cactus-graphmap-join - --binariesMode local - --giraffe - --maxCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M + --maxMemory \${GALAXY_MEMORY_MB:-8192}M + --outDir ./ --outName alignment --reference $aln_mode.ref_level - --vg alignment.vg - --outDir ./ ./jobStore + seqfile.txt #else if $aln_mode.aln_mode_select == 'interspecies': ## Run cactus normally cactus @@ -76,7 +40,9 @@ --maxCores \${GALAXY_SLOTS:-4} --maxMemory \${GALAXY_MEMORY_MB:-8192}M --workDir ./ - jobStore seqfile.txt alignment.hal + jobStore + seqfile.txt + alignment.full.hal #end if ]]></command> @@ -111,12 +77,12 @@ </param> <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/> </repeat> - <!-- add an option for root --> <!-- root mr --> </inputs> <outputs> - <data name="out_hal" format="h5" from_work_dir="alignment.hal" label="${tool.name} on ${on_string} (HAL file)" /> + <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)"> + </data> <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)" > <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter> </data> @@ -182,7 +148,7 @@ </repeat> <output name="out_hal"> <assert_contents> - <has_size value="2088959" delta="200000" /> + <has_size value="565214" delta="65214" /> </assert_contents> </output> <output name="out_gfa"> |
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| diff -r bdfbaf0c10aa -r 2263989660f5 macros.xml --- a/macros.xml Mon May 08 04:38:48 2023 +0000 +++ b/macros.xml Mon May 15 04:34:02 2023 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.5.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.09</token> <xml name="requirements"> <requirements> |