| Previous changeset 5:48c13389050d (2022-11-14) Next changeset 7:6ae5a7b5a0a2 (2023-02-09) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d |
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modified:
cactus_cactus.xml macros.xml test-data/evolverMammals_noroot.maf |
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| diff -r 48c13389050d -r a74dbfee5a86 cactus_cactus.xml --- a/cactus_cactus.xml Mon Nov 14 06:03:59 2022 +0000 +++ b/cactus_cactus.xml Thu Jan 12 02:00:52 2023 +0000 |
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| @@ -1,5 +1,5 @@ <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> - <description>whole-genome multiple sequence alignment.</description> + <description>whole-genome multiple sequence alignment</description> <macros> <import>macros.xml</import> </macros> @@ -61,15 +61,13 @@ && cactus-graphmap-join --binariesMode local - --gfaffix --giraffe --maxCores \${GALAXY_SLOTS:-4} --maxMemory \${GALAXY_MEMORY_MB:-8192}M - --outDir ./ --outName alignment --reference $aln_mode.ref_level --vg alignment.vg - --wlineSep "." + --outDir ./ ./jobStore #else if $aln_mode.aln_mode_select == 'interspecies': ## Run cactus normally @@ -92,14 +90,28 @@ <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'." /> + <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="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> </when> </conditional> <repeat name="in_seqs" title="Input genome"> - <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree."> + <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="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> </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> @@ -138,7 +150,7 @@ </repeat> <output name="out_hal"> <assert_contents> - <has_size value="4783905" delta="200000" /> + <has_size value="4472551" delta="200000" /> </assert_contents> </output> </test> @@ -235,12 +247,19 @@ </test> </tests> <help><![CDATA[ + +.. class:: infomark + **What it does** `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a reference-free whole-genome multiple alignment program. It can be used to progressively align a large number of genomes. +----- + +.. class:: infomark + **Usage** **Between-species mode (Progressive Cactus)** @@ -253,9 +272,9 @@ A Newick-formatted tree for human, chimp and gorilla genomes looks like this: -:: + :: - (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831); + (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831); The numbers are the branch lengths. @@ -270,7 +289,11 @@ pangenome mode, select ‘Within-species’ in the ‘Alignment mode’ dropdown. -Unlike Between-species mode, Within-species mode depends on a predetermined reference genome +Unlike Between-species mode, Within-species mode depends on a predetermined reference genome. + +----- + +.. class:: infomark **Input** @@ -281,6 +304,10 @@ fasta files that match the leaves on the guide tree. In the example above, you would use the label ‘human’ for the human fasta file. +----- + +.. class:: infomark + **Output** The main output of Cactus is in `HAL |
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| diff -r 48c13389050d -r a74dbfee5a86 macros.xml --- a/macros.xml Mon Nov 14 06:03:59 2022 +0000 +++ b/macros.xml Thu Jan 12 02:00:52 2023 +0000 |
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| @@ -1,13 +1,12 @@ <macros> - <token name="@TOOL_VERSION@">2.2.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.4.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.09</token> - <token name="@DIGEST@">b22eb2ef1d8c6f152d12d0e4300ac68affea5aafb2f7022f9078e8e72e41654d</token> <xml name="requirements"> <requirements> <!-- Cactus is not in bioconda --> <!-- Devoper provides a Docker container --> - <container type="docker">quay.io/comparative-genomics-toolkit/cactus@sha256:@DIGEST@</container> + <container type="docker">quay.io/comparative-genomics-toolkit/cactus:v@TOOL_VERSION@</container> </requirements> </xml> <xml name="citations"> |
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| diff -r 48c13389050d -r a74dbfee5a86 test-data/evolverMammals_noroot.maf --- a/test-data/evolverMammals_noroot.maf Mon Nov 14 06:03:59 2022 +0000 +++ b/test-data/evolverMammals_noroot.maf Thu Jan 12 02:00:52 2023 +0000 |
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| b'@@ -3422,6 +3422,70 @@\n s\tsimRat_chr6.simRat.chr6\t11039\t11\t+\t647215\tACAATCTCTTA\n \n a\n+s\tsimMouse_chr6.simMouse.chr6\t11603\t5\t+\t636262\tATCCC\n+s\tAnc0.Anc0refChr2\t6528\t5\t+\t17989\tATCCC\n+s\tAnc1.Anc1refChr6\t34612\t5\t+\t197743\tATCCC\n+s\tAnc2.Anc2refChr17\t28482\t5\t+\t28526\tATACA\n+s\tmr.mrrefChr0\t10664\t5\t+\t130230\tATCCC\n+s\tmr.mrrefChr0\t119688\t5\t-\t130230\tATCCC\n+s\tmr.mrrefChr5\t220265\t5\t+\t294540\tATCTC\n+s\tsimCow_chr6.simCow.chr6\t346008\t5\t+\t602619\tGCACT\n+s\tsimDog_chr6.simDog.chr6\t336875\t5\t+\t593897\tATACA\n+s\tsimMouse_chr6.simMouse.chr6\t373650\t5\t+\t636262\tATCTC\n+s\tsimMouse_chr6.simMouse.chr6\t624781\t5\t-\t636262\tATCCC\n+s\tsimRat_chr6.simRat.chr6\t365749\t5\t+\t647215\tATCTC\n+s\tsimRat_chr6.simRat.chr6\t636287\t5\t-\t647215\tCTCCC\n+s\tsimRat_chr6.simRat.chr6\t11050\t5\t+\t647215\tACCCC\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t11608\t1\t+\t636262\tA\n+s\tAnc0.Anc0refChr2\t6533\t1\t+\t17989\tA\n+s\tAnc1.Anc1refChr6\t34617\t1\t+\t197743\tA\n+s\tAnc2.Anc2refChr17\t28491\t1\t+\t28526\tA\n+s\tmr.mrrefChr0\t10669\t1\t+\t130230\tA\n+s\tmr.mrrefChr0\t119693\t1\t-\t130230\tA\n+s\tmr.mrrefChr5\t220270\t1\t+\t294540\tA\n+s\tsimCow_chr6.simCow.chr6\t346017\t1\t+\t602619\tA\n+s\tsimDog_chr6.simDog.chr6\t336884\t1\t+\t593897\tA\n+s\tsimMouse_chr6.simMouse.chr6\t373655\t1\t+\t636262\tA\n+s\tsimMouse_chr6.simMouse.chr6\t624786\t1\t-\t636262\tA\n+s\tsimRat_chr6.simRat.chr6\t365754\t1\t+\t647215\tA\n+s\tsimRat_chr6.simRat.chr6\t636292\t1\t-\t647215\tA\n+s\tsimRat_chr6.simRat.chr6\t11055\t1\t+\t647215\tA\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t11609\t3\t+\t636262\tACC\n+s\tAnc0.Anc0refChr2\t6534\t3\t+\t17989\tAGC\n+s\tAnc1.Anc1refChr6\t34618\t3\t+\t197743\tAGC\n+s\tAnc2.Anc2refChr17\t28492\t3\t+\t28526\tAGA\n+s\tmr.mrrefChr0\t10670\t3\t+\t130230\tACC\n+s\tmr.mrrefChr0\t119694\t3\t-\t130230\tGGT\n+s\tmr.mrrefChr5\t220271\t3\t+\t294540\tAGC\n+s\tsimCow_chr6.simCow.chr6\t346018\t3\t+\t602619\tAGA\n+s\tsimDog_chr6.simDog.chr6\t336885\t3\t+\t593897\tAGA\n+s\tsimMouse_chr6.simMouse.chr6\t373656\t3\t+\t636262\tAGC\n+s\tsimMouse_chr6.simMouse.chr6\t624787\t3\t-\t636262\tGGT\n+s\tsimRat_chr6.simRat.chr6\t365755\t3\t+\t647215\tAGA\n+s\tsimRat_chr6.simRat.chr6\t636293\t3\t-\t647215\tGGC\n+s\tsimRat_chr6.simRat.chr6\t11058\t3\t+\t647215\tATC\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t11612\t3\t+\t636262\tTCA\n+s\tAnc0.Anc0refChr2\t6537\t3\t+\t17989\tTCA\n+s\tAnc1.Anc1refChr6\t34621\t3\t+\t197743\tTCA\n+s\tAnc2.Anc2refChr17\t28495\t3\t+\t28526\tTCA\n+s\tmr.mrrefChr0\t10673\t3\t+\t130230\tTCA\n+s\tmr.mrrefChr0\t119697\t3\t-\t130230\tTCA\n+s\tmr.mrrefChr5\t220274\t3\t+\t294540\tCCA\n+s\tsimCow_chr6.simCow.chr6\t346021\t3\t+\t602619\tTAA\n+s\tsimDog_chr6.simDog.chr6\t336888\t3\t+\t593897\tTCA\n+s\tsimMouse_chr6.simMouse.chr6\t373659\t3\t+\t636262\tCCA\n+s\tsimMouse_chr6.simMouse.chr6\t624790\t3\t-\t636262\tTCA\n+s\tsimRat_chr6.simRat.chr6\t365758\t3\t+\t647215\tCTA\n+s\tsimRat_chr6.simRat.chr6\t636296\t3\t-\t647215\tTCA\n+s\tsimRat_chr6.simRat.chr6\t11067\t3\t+\t647215\tTCA\n+\n+a\n s\tsimMouse_chr6.simMouse.chr6\t11615\t1\t+\t636262\tG\n s\tmr.mrrefChr0\t10676\t1\t+\t130230\tG\n s\tsimRat_chr6.simRat.chr6\t11070\t1\t+\t647215\tG\n@@ -3483,7 +3547,22 @@\n s\tsimRat_chr6.simRat.chr6\t11078\t4\t+\t647215\tAAGG\n \n a\n-s\tsimMouse_chr6.simMouse.chr6\t11631\t1\t+\t636262\tT\n+s\tsimMouse_chr6.simMouse.chr6\t11627\t7\t+\t636262\tATACTTT\n+s\tAnc0.Anc0refChr2\t6551\t6\t+\t17989\tACAG-GG\n+s\tAnc1.Anc1refChr2\t113615\t6\t-\t144309\tACAG-GG\n+s\tAnc1.Anc1refChr6\t34635\t6\t+\t197743\tATAC-GT\n+s\tAnc2.Anc2refChr0\t51606\t6\t+\t56053\tACAG-GG\n+s\tmr.mrrefChr0\t10688\t6\t+\t130230\tATAC-TT\n+s\tmr.mrrefChr0\t119700\t6\t-\t130230\tATAC-GC\n+s\tmr.mrrefChr5\t220294\t6\t+\t294540\tAGGG-GT\n+s\tsimCow_chr6.simCow.chr6\t55081\t6\t+\t602619\tACAG-GG\n+s\tsimDog_chr6.simDog.chr6\t48656\t6\t+\t593897\tACAG-GG\n+s\tsimHuman_chr6.simHuman.chr6\t551636\t6\t-\t601863\tACAG-AG\n+s\tsimMouse_chr6.simMouse.chr6\t373679\t6\t+\t636262\tAGGG-GT\n+s\tsimMouse_chr6.simMouse.chr6\t624793\t6\t-\t636262\tATAC-GC\n+s\tsimRat_chr6.simRat.chr6\t365778\t6\t+\t647215\tAGAG-AT\n+s\tsimRat_chr6.simRat.chr6\t636299\t6\t-\t647215\tACAC-GC\n+s\tsimRat_chr6.simRat.chr6\t11082\t6\t+\t647215\tATAC-TT\n \n a\n s\tsimMouse_chr6.simMouse.chr6\t11634\t3\t+\t636262\tTCA\n@@ -3501,6 +3580,114 @@\n s\tsimRat_chr6.simRat.chr6\t11088\t3\t+\t647215\tTCA\n \n a\n+s\tsimMouse_chr6.simMouse.chr6\t11637\t9\t+\t636262\tGTATTAGCA\n+s\tAnc0.Anc0refChr2\t6560\t9\t+\t17989\tGTGTTAAGA\n+s\tAnc1.Anc1refChr2\t113624\t9\t-\t144309\tGTGTTAAGA\n+s\tAnc1.Anc1ref'..b'181027\tCGTA\n+s\tmr.mrrefChr5\t198699\t4\t-\t294540\tCGTA\n+s\tsimMouse_chr6.simMouse.chr6\t167390\t4\t-\t636262\tCGTA\n+s\tsimMouse_chr6.simMouse.chr6\t27016\t4\t-\t636262\tCGTA\n+s\tsimMouse_chr6.simMouse.chr6\t393516\t4\t-\t636262\tTGTA\n+s\tsimRat_chr6.simRat.chr6\t168404\t4\t-\t647215\tTGTA\n+s\tsimRat_chr6.simRat.chr6\t563417\t4\t+\t647215\tTGTA\n+s\tsimRat_chr6.simRat.chr6\t580309\t4\t+\t647215\tCATA\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t635541\t18\t+\t636262\tCGCTTTGTTCACGACTTC\n+s\tAnc1.Anc1refChr6\t75781\t18\t-\t197743\tTGCTTTGTTTGCGACTTT\n+s\tmr.mrrefChr3\t156452\t18\t-\t181027\tTGCTCTGTTTGCAACTTT\n+s\tmr.mrrefChr3\t23861\t18\t-\t181027\tTGCTTTGTTTGCGGCTTC\n+s\tmr.mrrefChr5\t198703\t18\t-\t294540\tCGCTTTGTTTGCGACTTT\n+s\tsimMouse_chr6.simMouse.chr6\t167394\t18\t-\t636262\tTGCTCTGTTTGCAACTTT\n+s\tsimMouse_chr6.simMouse.chr6\t27020\t18\t-\t636262\tTGCTTTGTTTGCGGCTTC\n+s\tsimMouse_chr6.simMouse.chr6\t393520\t18\t-\t636262\tCGCTTTGTTTGTGAATTT\n+s\tsimRat_chr6.simRat.chr6\t168408\t18\t-\t647215\tTACTTTGCTTGCAACTTT\n+s\tsimRat_chr6.simRat.chr6\t563421\t18\t+\t647215\tTGCCTTGTTTGTGACTTC\n+s\tsimRat_chr6.simRat.chr6\t294603\t18\t-\t647215\tTACATTGTTTGCGACTTA\n+s\tsimRat_chr6.simRat.chr6\t580313\t17\t+\t647215\tTGCTTCGTTTGCGACTT-\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t635559\t4\t+\t636262\tGAAG\n+s\tAnc1.Anc1refChr6\t75799\t4\t-\t197743\tGAAG\n+s\tmr.mrrefChr3\t156470\t4\t-\t181027\tGAAG\n+s\tmr.mrrefChr5\t198721\t4\t-\t294540\tGAAG\n+s\tsimMouse_chr6.simMouse.chr6\t167412\t4\t-\t636262\tGAAG\n+s\tsimMouse_chr6.simMouse.chr6\t393538\t4\t-\t636262\tGAAG\n+s\tsimRat_chr6.simRat.chr6\t168426\t4\t-\t647215\tGAAG\n+s\tsimRat_chr6.simRat.chr6\t294621\t4\t-\t647215\tGAAG\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t635563\t2\t+\t636262\tTC\n+s\tAnc1.Anc1refChr6\t75803\t2\t-\t197743\tCC\n+s\tmr.mrrefChr3\t156474\t2\t-\t181027\tCC\n+s\tmr.mrrefChr5\t198725\t2\t-\t294540\tTC\n+s\tsimMouse_chr6.simMouse.chr6\t167417\t2\t-\t636262\tCC\n+s\tsimMouse_chr6.simMouse.chr6\t393542\t2\t-\t636262\tTC\n+s\tsimRat_chr6.simRat.chr6\t168430\t2\t-\t647215\tCC\n+s\tsimRat_chr6.simRat.chr6\t294625\t2\t-\t647215\tCC\n+s\tsimRat_chr6.simRat.chr6\t580330\t2\t+\t647215\tCC\n+\n+a\n+s\tsimMouse_chr6.simMouse.chr6\t635565\t2\t+\t636262\tTC\n+s\tAnc0.Anc0refChr3\t133326\t1\t-\t222631\t-C\n+s\tAnc1.Anc1refChr6\t75805\t2\t-\t197743\tCC\n+s\tAnc2.Anc2refChr1\t142501\t1\t-\t142988\t-C\n+s\tmr.mrrefChr3\t156476\t2\t-\t181027\tCC\n+s\tmr.mrrefChr5\t198727\t2\t-\t294540\tTC\n+s\tsimCow_chr6.simCow.chr6\t148730\t1\t-\t602619\t-C\n+s\tsimDog_chr6.simDog.chr6\t448535\t1\t+\t593897\t-C\n+s\tsimMouse_chr6.simMouse.chr6\t167419\t2\t-\t636262\tCC\n+s\tsimRat_chr6.simRat.chr6\t168432\t2\t-\t647215\tCT\n+s\tsimRat_chr6.simRat.chr6\t294630\t2\t-\t647215\tAC\n+s\tsimRat_chr6.simRat.chr6\t580332\t1\t+\t647215\tT-\n \n a\n s\tsimMouse_chr6.simMouse.chr6\t635567\t2\t+\t636262\tTG\n@@ -238522,27 +256144,16 @@\n s\tsimRat_chr6.simRat.chr6\t294632\t2\t-\t647215\tAg\n \n a\n-s\tsimMouse_chr6.simMouse.chr6\t635569\t2\t+\t636262\tGA\n-s\tAnc0.Anc0refChr5\t25915\t2\t-\t87904\tGC\n-s\tAnc1.Anc1refChr7\t27595\t2\t+\t47259\tGC\n-s\tAnc2.Anc2refChr15\t27830\t2\t-\t86568\tGC\n-s\tmr.mrrefChr5\t198731\t2\t-\t294540\tga\n-s\tsimCow_chr6.simCow.chr6\t363177\t2\t-\t602619\tGA\n-s\tsimDog_chr6.simDog.chr6\t362358\t2\t-\t593897\tTC\n-s\tsimHuman_chr6.simHuman.chr6\t280430\t2\t+\t601863\tGC\n-s\tsimRat_chr6.simRat.chr6\t294634\t2\t-\t647215\tgt\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t635571\t2\t+\t636262\tTT\n-s\tAnc0.Anc0refChr5\t25917\t2\t-\t87904\tCA\n-s\tAnc1.Anc1refChr7\t27597\t2\t+\t47259\tCA\n-s\tAnc2.Anc2refChr15\t27832\t2\t-\t86568\tCA\n-s\tmr.mrrefChr5\t198733\t2\t-\t294540\tTT\n-s\tsimCow_chr6.simCow.chr6\t363179\t2\t-\t602619\tCA\n-s\tsimDog_chr6.simDog.chr6\t362360\t2\t-\t593897\tCA\n-s\tsimHuman_chr6.simHuman.chr6\t280432\t2\t+\t601863\tCA\n-s\tsimRat_chr6.simRat.chr6\t294636\t2\t-\t647215\tgg\n-s\tsimRat_chr6.simRat.chr6\t580333\t2\t+\t647215\tTT\n+s\tsimMouse_chr6.simMouse.chr6\t635569\t4\t+\t636262\tGATT\n+s\tAnc0.Anc0refChr5\t25915\t4\t-\t87904\tGCCA\n+s\tAnc1.Anc1refChr7\t27595\t4\t+\t47259\tGCCA\n+s\tAnc2.Anc2refChr15\t27830\t4\t-\t86568\tGCCA\n+s\tmr.mrrefChr5\t198731\t4\t-\t294540\tgaTT\n+s\tsimCow_chr6.simCow.chr6\t363177\t4\t-\t602619\tGACA\n+s\tsimDog_chr6.simDog.chr6\t362358\t4\t-\t593897\tTCCA\n+s\tsimHuman_chr6.simHuman.chr6\t280430\t4\t+\t601863\tGCCA\n+s\tsimRat_chr6.simRat.chr6\t294634\t4\t-\t647215\tgtgg\n+s\tsimRat_chr6.simRat.chr6\t580333\t2\t+\t647215\t--TT\n \n a\n s\tsimMouse_chr6.simMouse.chr6\t635573\t5\t+\t636262\tTACTA\n' |