Mercurial > repos > galaxy-australia > cactus_cactus

diff cactus_cactus.xml @ 12:2263989660f5 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cb75f42cdcae1a92023e6e5b33a8a260877d76fe
author galaxy-australia
date Mon, 15 May 2023 04:34:02 +0000
parents 6ae5a7b5a0a2
children 9eeb13a92d79
line wrap: on
line diff
--- 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">