Mercurial > repos > iuc > meryl_trio_mode
annotate trio-mode.xml @ 0:c85aec7804a4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
author | iuc |
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date | Thu, 25 Apr 2024 21:01:24 +0000 |
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0
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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1 <tool id="meryl_trio_mode" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@"> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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2 <description>build hap-mers databases for trios</description> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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3 <macros> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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5 </macros> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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6 <expand macro="edam_ontology"/> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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7 <xrefs> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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8 <xref type="bio.tools">meryl</xref> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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9 </xrefs> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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10 <expand macro="requirements"/> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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11 <version_command>meryl --version</version_command> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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12 <command detect_errors="exit_code"><![CDATA[ |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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14 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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15 #if $options_kmer_size.kmer_size == 'estimate' |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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16 #from math import log |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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17 #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4)) |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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18 #elif $options_kmer_size.kmer_size == 'provide' |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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19 #set size=$options_kmer_size.input_kmer_size |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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20 #end if |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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21 #for $i, $read in enumerate($paternal_reads): |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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22 mkdir 'paternal${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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23 ln -s '$read' ./input_paternal_${i}.${read.ext} && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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24 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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25 #end for |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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26 meryl union-sum paternal*.meryl output pat.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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27 #for $i, $read in enumerate($maternal_reads): |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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28 mkdir 'maternal${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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29 ln -s '$read' ./input_maternal_${i}.${read.ext} && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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30 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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31 #end for |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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32 meryl union-sum maternal*.meryl output mat.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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33 #for $i, $read in enumerate($child_reads): |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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34 mkdir 'child${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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35 ln -s '$read' ./input_child_${i}.${read.ext} && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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36 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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37 #end for |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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38 meryl union-sum child*.meryl output child.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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39 meryl histogram child.meryl > read-db.hist && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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40 tar -czf 'read-db.meryldb' child.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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41 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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42 ## mat specific kmers |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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43 meryl difference mat.meryl pat.meryl output mat.only.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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44 meryl histogram mat.only.meryl > mat.only.hist && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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45 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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46 VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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47 meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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48 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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49 ## pat specific kmers |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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50 meryl difference pat.meryl mat.meryl output pat.only.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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51 meryl histogram pat.only.meryl > pat.only.hist && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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52 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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53 VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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54 meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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55 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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56 ## shared kmers |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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57 meryl intersect output shared.meryl mat.meryl pat.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
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58 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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59 ## mat hapmers |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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60 meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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61 meryl histogram mat.inherited.meryl > mat.inherited.hist && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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62 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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63 VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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64 meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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65 tar -czf 'mat.meryldb' mat.hapmer.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
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66 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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67 ## pat hapmers |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
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68 meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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69 meryl histogram pat.inherited.meryl > pat.inherited.hist && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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changeset
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70 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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71 VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
diff
changeset
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72 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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73 tar -czf 'pat.meryldb' pat.hapmer.meryl && |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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74 |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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75 echo 'K-mer size: ${size}' |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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76 ]]></command> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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77 <inputs> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
parents:
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78 <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly"/> |
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79 <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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80 <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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81 <conditional name="options_kmer_size"> |
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82 <param name="kmer_size" type="select" label="K-mer size selector"> |
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83 <option value="provide">Set a k-mer size</option> |
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84 <option value="estimate">Estimate the best k-mer size</option> |
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85 </param> |
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86 <when value="provide"> |
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87 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)."/> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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88 </when> |
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89 <when value="estimate"> |
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90 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/> |
c85aec7804a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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91 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/> |
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92 </when> |
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93 </conditional> |
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94 </inputs> |
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95 <outputs> |
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96 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"/> |
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97 <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"/> |
c85aec7804a4
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98 <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"/> |
c85aec7804a4
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99 <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"/> |
c85aec7804a4
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100 <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb"/> |
c85aec7804a4
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101 <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"/> |
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102 </outputs> |
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103 <tests> |
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104 <test expect_num_outputs="6"> |
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105 <conditional name="options_kmer_size"> |
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106 <param name="kmer_size" value="provide"/> |
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107 <param name="input_kmer_size" value="21"/> |
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108 </conditional> |
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109 <param name="maternal_reads" value="maternal.fasta"/> |
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110 <param name="paternal_reads" value="paternal.fasta"/> |
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111 <param name="child_reads" value="child.fasta"/> |
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112 <output name="read_db" ftype="meryldb"> |
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113 <assert_contents> |
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114 <has_size value="3362942" delta="2000"/> |
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115 <expand macro="meryldb_archive_assumptions"/> |
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116 </assert_contents> |
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117 </output> |
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118 <output name="read_db_hist" file="output_23.read-db.hist"/> |
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119 <output name="pat_db" ftype="meryldb"> |
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120 <assert_contents> |
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121 <has_size value="120610" delta="400"/> |
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122 <expand macro="meryldb_archive_assumptions"/> |
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123 </assert_contents> |
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124 </output> |
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125 <output name="pat_db_hist" file="output_23.pat.hist"/> |
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126 <output name="mat_db" ftype="meryldb"> |
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127 <assert_contents> |
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128 <has_size value="67883" delta="300"/> |
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129 <expand macro="meryldb_archive_assumptions"/> |
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130 </assert_contents> |
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131 </output> |
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132 <output name="mat_db_hist" file="output_23.mat.hist"/> |
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133 </test> |
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134 </tests> |
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135 <help> |
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136 |
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137 .. class:: infomark |
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138 |
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139 **Purpose** |
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140 |
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141 Meryl is the k-mer counter. This tool builds hap-mer databases for trios, in accordance |
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142 with `merqury's recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_ |
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143 |
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144 </help> |
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145 <expand macro="citations"/> |
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146 </tool> |