Mercurial > repos > galaxy-australia > cactus_cactus
diff cactus_cactus.xml @ 15:098506c54016 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
| author | iuc |
|---|---|
| date | Thu, 08 Feb 2024 08:52:28 +0000 |
| parents | 9eeb13a92d79 |
| children |
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--- a/cactus_cactus.xml Mon Aug 28 23:10:21 2023 +0000 +++ b/cactus_cactus.xml Thu Feb 08 08:52:28 2024 +0000 @@ -6,7 +6,6 @@ <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - export TMPDIR=\${_GALAXY_JOB_TMP_DIR} && ## Set up seqfile @@ -30,7 +29,7 @@ --reference $aln_mode.ref_level --binariesMode local --maxCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M + --maxMemory \${GALAXY_MEMORY_MB:-16384}M --outDir ./ --outName alignment jobStore @@ -40,7 +39,7 @@ cactus --binariesMode local --maxCores \${GALAXY_SLOTS:-4} - --maxMemory \${GALAXY_MEMORY_MB:-8192}M + --maxMemory \${GALAXY_MEMORY_MB:-16384}M --workDir ./ jobStore seqfile.txt @@ -55,13 +54,13 @@ <option value="intraspecies">Within-species</option> </param> <when value="interspecies"> - <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" /> + <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes"/> </when> <when value="intraspecies"> <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'."> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="_" /> + <add value="_"/> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> @@ -72,7 +71,7 @@ <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree."> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="_" /> + <add value="_"/> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> @@ -85,7 +84,7 @@ <outputs> <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${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 ${on_string} (GFA file)" > + <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)"> <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter> </data> </outputs> @@ -118,7 +117,7 @@ </repeat> <output name="out_hal"> <assert_contents> - <has_size value="4472551" delta="200000" /> + <has_size value="4472551" delta="200000"/> </assert_contents> </output> </test> @@ -150,41 +149,12 @@ </repeat> <output name="out_hal"> <assert_contents> - <has_size value="565214" delta="65214" /> + <has_size value="565214" delta="65214"/> </assert_contents> </output> <output name="out_gfa"> <assert_contents> - <has_size value="173000" delta="200000" /> - </assert_contents> - </output> - </test> - <!-- compressed input --> - <test expect_num_outputs="2"> - <conditional name="aln_mode"> - <param name="aln_mode_select" value="intraspecies"/> - <param name="ref_level" value="germ_25"/> - </conditional> - <repeat name="in_seqs"> - <param name="label" value="germ_25"/> - <param name="fasta" value="germ_25.fasta.gz"/> - </repeat> - <repeat name="in_seqs"> - <param name="label" value="vulg_25"/> - <param name="fasta" value="vulg_25.fasta.gz"/> - </repeat> - <repeat name="in_seqs"> - <param name="label" value="pens_25"/> - <param name="fasta" value="pens_25.fasta.gz"/> - </repeat> - <output name="out_hal"> - <assert_contents> - <has_size value="6235006" delta="200000" /> - </assert_contents> - </output> - <output name="out_gfa"> - <assert_contents> - <has_size value="5771414" delta="200000" /> + <has_size value="173000" delta="200000"/> </assert_contents> </output> </test> @@ -204,17 +174,17 @@ </repeat> <output name="out_hal"> <assert_contents> - <has_size value="3382274" delta="200000" /> + <has_size value="3382274" delta="200000"/> </assert_contents> </output> <output name="out_gfa"> <assert_contents> - <has_size value="764748" delta="200000" /> + <has_size value="764748" delta="200000"/> </assert_contents> </output> </test> </tests> - <help><![CDATA[ + <help><![CDATA[ .. class:: infomark