Mercurial > repos > iuc > meryl
annotate meryl.xml @ 2:35ac9de60bec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
author | iuc |
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date | Fri, 09 Apr 2021 13:21:51 +0000 |
parents | e5b18909f73d |
children | 9f7a227436d6 |
rev | line source |
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0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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1 <tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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2 <description>a genomic k-mer counter and sequence utility</description> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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3 <macros> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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4 <import>macros.xml</import> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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5 </macros> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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6 <expand macro='edam_ontology' /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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7 <expand macro='requirements' /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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8 <version_command>meryl --version</version_command> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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9 <command detect_errors='exit_code'><![CDATA[ |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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10 #if $operation_type.command_type == 'count-kmers' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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11 #if $operation_type.options_kmer_size.kmer_size == 'estimate' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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12 #from math import log |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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13 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4)) |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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14 #elif $operation_type.options_kmer_size.kmer_size == 'provide' |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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15 #set size=$operation_type.options_kmer_size.input_kmer_size |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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16 #end if |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
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17 meryl |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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18 $operation_type.count_operations |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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19 k=$size |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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20 memory=\${GALAXY_MEMORY_GB:-1} |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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21 threads=\${GALAXY_SLOTS:-1} |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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22 $operation_type.input_reads |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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23 output read-db.meryl && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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24 echo 'K-mer size: ${size}' && |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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25 tar -zcf read-db.meryldb read-db.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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26 #elif $operation_type.command_type == 'filter-kmers' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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27 mkdir -p ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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28 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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29 mv ./temp_db/* tmp.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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30 meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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31 $operation_type.filter_operations |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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32 $operation_type.N |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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33 tmp.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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34 output read-db.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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35 tar -zcf read-db.meryldb read-db.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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36 #elif $operation_type.command_type == 'arithmetic-kmers' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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37 mkdir -p ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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38 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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39 mv ./temp_db/* tmp.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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40 meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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41 $operation_type.arithmetic_operations |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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42 $operation_type.X |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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43 tmp.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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44 output read-db.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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45 tar -zcf read-db.meryldb read-db.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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46 #elif $operation_type.command_type == 'groups-kmers' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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47 mkdir -p ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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48 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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49 mv ./temp_db/* tmp_01.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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50 tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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51 mv ./temp_db/* tmp_02.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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52 meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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53 $operation_type.groups_operations |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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54 tmp_01.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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55 tmp_02.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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56 output read-db.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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57 tar -zcf read-db.meryldb read-db.meryl |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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58 #elif $operation_type.command_type == 'histogram-kmers' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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59 mkdir -p ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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60 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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61 mv ./temp_db/* tmp.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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62 meryl histogram tmp.meryl > read-db.hist |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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63 #elif $operation_type.command_type == 'trio-mode' |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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64 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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65 #if $operation_type.options_kmer_size.kmer_size == 'estimate' |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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66 #from math import log |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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67 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4)) |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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68 #elif $operation_type.options_kmer_size.kmer_size == 'provide' |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
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69 #set size=$operation_type.options_kmer_size.input_kmer_size |
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
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70 #end if |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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71 #for $i, $read in enumerate($paternal_reads): |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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72 mkdir 'paternal{$i}.meryl' && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
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73 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' && |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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74 #end for |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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75 meryl union-sum paternal*.meryl output pat.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
76 #for $i, $read in enumerate($maternal_reads): |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
77 mkdir 'maternal{$i}.meryl' && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
diff
changeset
|
78 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' && |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
79 #end for |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
80 meryl union-sum maternal*.meryl output mat.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
81 #for $i, $read in enumerate($child_reads): |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
82 mkdir 'child{$i}.meryl' && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
diff
changeset
|
83 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' && |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
84 #end for |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
85 meryl union-sum child*.meryl output child.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
86 ## mat specific kmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
87 meryl difference mat.meryl pat.meryl output mat.only.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
88 meryl histogram mat.only.meryl > mat.only.hist && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
89 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
90 VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
91 meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
92 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
93 ## pat specific kmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
94 meryl difference pat.meryl mat.meryl output pat.only.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
95 meryl histogram pat.only.meryl > pat.only.hist && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
96 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
97 VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
98 meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
99 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
100 ## shared kmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
101 meryl intersect output shared.meryl mat.meryl pat.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
102 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
103 ## mat hapmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
104 meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
105 meryl histogram mat.inherited.meryl > mat.inherited.hist && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
106 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
107 VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
108 meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
109 tar -czf 'mat.meryldb' mat.hapmer.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
110 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
111 ## pat hapmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
112 meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
113 meryl histogram pat.inherited.meryl > pat.inherited.hist && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
114 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
115 VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
116 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
117 tar -czf 'pat.meryldb' pat.hapmer.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
118 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
119 ## shared hapmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
120 meryl intersect output shared.inherited.meryl child.meryl shared.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
121 meryl histogram shared.inherited.meryl > shared.inherited.hist && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
122 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
123 VAR=`sed -n 2p shared.inherited.ploidy | awk '{print \$NF}'` && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
124 meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
125 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
126 ## child hapmers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
127 meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
128 meryl difference output read.only.meryl child.meryl child.inherited.meryl && |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
129 tar -czf 'read-db.meryldb' read.only.meryl && |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
parents:
1
diff
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|
130 echo 'K-mer size: ${size}' |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
131 #end if |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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|
132 ]]> </command> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
133 <inputs> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
134 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
135 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
136 <option value="count-kmers">Count operations</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
137 <option value="filter-kmers">Filter operations</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
138 <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
139 <option value="groups-kmers">Operations on sets of k-mers</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
140 <option value="histogram-kmers">Generate histogram dataset</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
141 <option value="trio-mode">Build hap-mer dbs for trios</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
142 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
143 <when value="count-kmers"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
144 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
145 <option value="count">Count: count the occurrences of canonical k-mers</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
146 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
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|
147 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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|
148 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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|
149 <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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150 <conditional name="options_kmer_size"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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151 <param name="kmer_size" type="select" label="K-mer size selector"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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152 <option value="provide">Set a k-mer size</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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153 <option value="estimate">Estimate the best k-mer size</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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154 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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155 <when value="provide"> |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
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156 <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).." /> |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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157 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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158 <when value="estimate"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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159 <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." /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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160 <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." /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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161 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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162 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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163 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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164 <when value="filter-kmers"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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165 <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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166 <option value="less-than">Less-than: return k-mers that occur fewer than N times in the input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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167 <option value="greater-than">Greater-than: return k-mers that occur more than N times in the input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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168 <option value="equal-to">Equal-to: return k-mers that occur exactly N times in the input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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169 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly N times in the input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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170 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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171 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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172 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Filter value" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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173 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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174 <when value="arithmetic-kmers"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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175 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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176 <option value="increase">Increase: add x to the count of each k-mer</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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177 <option value="decrease">Decrease: subsctract x from the count of each k-mer</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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178 <option value="multiply">Multiply: multiply the count of each k-mer by x</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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179 <option value="divide">Divide: divide the count of each k-mer by x</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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180 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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181 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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182 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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183 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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184 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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185 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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186 <when value="groups-kmers"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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187 <param name="groups_operations" type="select" label="Operations on sets of kmers" help="Select an operation to be executed"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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188 <option value="union">Union: return k-mers that occur in any input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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189 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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190 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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191 <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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192 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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193 <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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194 <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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195 <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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196 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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197 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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198 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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199 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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200 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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201 <param name="input_meryldb_03" type="data" format="meryldb" label="Input meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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202 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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203 <when value="histogram-kmers"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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204 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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205 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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206 <when value="trio-mode"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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207 <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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208 <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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209 <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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210 <conditional name="options_kmer_size"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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211 <param name="kmer_size" type="select" label="K-mer size selector"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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212 <option value="provide">Set a k-mer size</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
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213 <option value="estimate">Estimate the best k-mer size</option> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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214 </param> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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215 <when value="provide"> |
2
35ac9de60bec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
iuc
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216 <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)." /> |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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217 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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218 <when value="estimate"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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219 <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." /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
220 <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." /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
221 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
222 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
223 </when> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
224 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
225 </inputs> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
226 <outputs> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
227 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
228 <filter>operation_type["command_type"] != "histogram-kmers"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
229 </data> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
230 <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
231 <filter>operation_type["command_type"] == "histogram-kmers" or operation_type["command_type"] == "trio-mode"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
232 </data> |
1
e5b18909f73d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec"
iuc
parents:
0
diff
changeset
|
233 <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"> |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
234 <filter>operation_type["command_type"] == "trio-mode"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
235 </data> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
236 <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
237 <filter>operation_type["command_type"] == "trio-mode"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
238 </data> |
1
e5b18909f73d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec"
iuc
parents:
0
diff
changeset
|
239 <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb"> |
0
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
240 <filter>operation_type["command_type"] == "trio-mode"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
241 </data> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
242 <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
243 <filter>operation_type["command_type"] == "trio-mode"</filter> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
244 </data> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
245 </outputs> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
246 <tests> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
247 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
248 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
249 <param name="command_type" value="count-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
250 <param name="count_operation" value="count" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
251 <param name="input_reads" value="child.fasta" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
252 <conditional name="options_kmer_size"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
253 <param name="kmer_size" value="provide" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
254 <param name="input_kmer_size" value="7" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
255 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
256 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
257 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
258 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
259 <has_size value="22152" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
260 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
261 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
262 <assert_stdout> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
263 <has_line line="K-mer size: 7" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
264 </assert_stdout> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
265 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
266 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
267 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
268 <param name="command_type" value="filter-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
269 <param name="filter_operations" value="less-than" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
270 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
271 <param name="N" value="100" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
272 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
273 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
274 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
275 <has_size value="32077" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
276 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
277 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
278 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
279 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
280 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
281 <param name="command_type" value="filter-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
282 <param name="filter_operations" value="greater-than" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
283 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
284 <param name="N" value="80" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
285 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
286 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
287 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
288 <has_size value="49951" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
289 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
290 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
291 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
292 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
293 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
294 <param name="command_type" value="filter-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
295 <param name="filter_operations" value="equal-to" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
296 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
297 <param name="N" value="100" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
298 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
299 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
300 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
301 <has_size value="2621" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
302 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
303 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
304 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
305 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
306 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
307 <param name="command_type" value="filter-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
308 <param name="filter_operations" value="not-equal-to" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
309 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
310 <param name="N" value="100" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
311 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
312 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
313 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
314 <has_size value="59378" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
315 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
316 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
317 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
318 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
319 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
320 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
321 <param name="arithmetic_operations" value="increase" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
322 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
323 <param name="X" value="100000" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
324 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
325 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
326 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
327 <has_size value="59822" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
328 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
329 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
330 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
331 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
332 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
333 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
334 <param name="arithmetic_operations" value="decrease" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
335 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
336 <param name="X" value="100" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
337 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
338 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
339 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
340 <has_size value="42625" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
341 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
342 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
343 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
344 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
345 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
346 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
347 <param name="arithmetic_operations" value="multiply" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
348 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
349 <param name="X" value="3" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
350 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
351 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
352 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
353 <has_size value="60832" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
354 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
355 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
356 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
357 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
358 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
359 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
360 <param name="arithmetic_operations" value="divide" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
361 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
362 <param name="X" value="2" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
363 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
364 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
365 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
366 <has_size value="56569" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
367 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
368 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
369 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
370 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
371 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
372 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
373 <param name="arithmetic_operations" value="divide-round" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
374 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
375 <param name="X" value="2" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
376 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
377 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
378 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
379 <has_size value="56539" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
380 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
381 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
382 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
383 <!-- test 11 --> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
384 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
385 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
386 <param name="command_type" value="arithmetic-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
387 <param name="arithmetic_operations" value="modulo" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
388 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
389 <param name="X" value="3" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
390 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
391 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
392 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
393 <has_size value="37542" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
394 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
395 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
396 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
397 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
398 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
399 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
400 <param name="groups_operations" value="union" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
401 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
402 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
403 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
404 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
405 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
406 <has_size value="36417" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
407 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
408 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
409 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
410 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
411 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
412 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
413 <param name="groups_operations" value="union-min" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
414 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
415 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
416 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
417 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
418 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
419 <has_size value="59226" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
420 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
421 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
422 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
423 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
424 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
425 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
426 <param name="groups_operations" value="union-max" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
427 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
428 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
429 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
430 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
431 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
432 <has_size value="59234" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
433 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
434 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
435 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
436 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
437 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
438 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
439 <param name="groups_operations" value="union-sum" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
440 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
441 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
442 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
443 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
444 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
445 <has_size value="59004" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
446 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
447 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
448 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
449 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
450 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
451 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
452 <param name="groups_operations" value="intersect" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
453 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
454 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
455 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
456 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
457 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
458 <has_size value="14951" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
459 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
460 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
461 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
462 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
463 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
464 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
465 <param name="groups_operations" value="intersect-min" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
466 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
467 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
468 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
469 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
470 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
471 <has_size value="14957" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
472 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
473 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
474 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
475 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
476 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
477 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
478 <param name="groups_operations" value="intersect-max" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
479 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
480 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
481 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
482 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
483 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
484 <has_size value="14956" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
485 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
486 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
487 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
488 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
489 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
490 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
491 <param name="groups_operations" value="intersect-sum" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
492 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
493 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
494 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
495 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
496 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
497 <has_size value="14953" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
498 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
499 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
500 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
501 <!-- test 20 --> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
502 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
503 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
504 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
505 <param name="groups_operations" value="subtract" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
506 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
507 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
508 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
509 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
510 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
511 <has_size value="23999" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
512 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
513 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
514 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
515 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
516 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
517 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
518 <param name="groups_operations" value="difference" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
519 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
520 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
521 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
522 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
523 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
524 <has_size value="24016" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
525 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
526 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
527 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
528 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
529 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
530 <param name="command_type" value="groups-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
531 <param name="groups_operations" value="symmetric-difference" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
532 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
533 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
534 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
535 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
536 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
537 <has_size value="57455" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
538 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
539 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
540 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
541 <test expect_num_outputs="6"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
542 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
543 <param name="command_type" value="trio-mode" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
544 <param name="child_reads" value="child.fasta" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
545 <param name="paternal_reads" value="paternal.fasta" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
546 <param name="maternal_reads" value="maternal.fasta" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
547 <conditional name="options_kmer_size"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
548 <param name="kmer_size" value="provide" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
549 <param name="input_kmer_size" value="7" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
550 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
551 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
552 <output name="read_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
553 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
554 <has_size value="1573" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
555 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
556 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
557 <output name="read_db_hist" file="output_23.read-db.hist" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
558 <output name="pat_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
559 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
560 <has_size value="1779" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
561 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
562 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
563 <output name="pat_db_hist" file="output_23.pat.hist" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
564 <output name="mat_db" ftype="meryldb"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
565 <assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
566 <has_size value="1569" delta="300" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
567 </assert_contents> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
568 </output> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
569 <output name="mat_db_hist" file="output_23.mat.hist" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
570 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
571 <test expect_num_outputs="1"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
572 <conditional name="operation_type"> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
573 <param name="command_type" value="histogram-kmers" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
574 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
575 </conditional> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
576 <output name="read_db_hist" file="output_24.read-db.hist" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
577 </test> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
578 </tests> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
579 <help><![CDATA[ |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
580 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
581 .. class:: infomark |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
582 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
583 **Purpose** |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
584 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
585 Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application. |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
586 Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order. |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
587 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
588 In addition of generating count-databases, meryl can perform simple operations on it. |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
589 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
590 ----- |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
591 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
592 .. class:: infomark |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
593 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
594 **Basic functions** |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
595 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
596 The functions that meryl includes are described below: |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
597 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
598 :: |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
599 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
600 COUNT OPERATIONS |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
601 - Count: count the occurrences of canonical k-mers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
602 - Count-forward: count the occurreces of forward k-mers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
603 - Count-reverse: count the occurreces of reverse k-mers |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
604 FILTERING OPERATIONS |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
605 - Less-than: return k-mers that occur fewer than N times in the input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
606 - Greater-than: return k-mers that occur more than N times in the input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
607 - Equal-to: return k-mers that occur exactly N times in the input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
608 - Not-equal-to: return k-mers that do not occur exactly N times in the input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
609 ARITHMETIC OPERATIONS |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff
changeset
|
610 - Increase: add x to the count of each k-mer |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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611 - Decrease: subsctract x from the count of each k-mer |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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612 - Multiply: multiply the count of each k-mer by x |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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613 - Divide: divide the count of each k-mer by x |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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614 - Divide-round: divide the count of each k-mer by x and round th results |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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615 - Modulo: set the count of each k-mer to the remainder of the count divided by x |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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616 OPERATIONS ON SETS |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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617 - Union-min: return k-mers that occur in any input, set the count to the minimum count |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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618 - Union-max: return k-mers that occur in any input, set the count to the maximum count |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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619 - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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620 - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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621 - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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622 - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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623 - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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624 - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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625 - Difference: return k-mers that occur in the first input, but none of the other inputs |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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626 - Symmetric-difference: return k-mers that occur in exactly one input |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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627 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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628 ----- |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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629 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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630 .. class:: infomark |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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631 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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632 **Additional function: build hap-mers dbs for trios** |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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633 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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634 In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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635 with `merqury's recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_ |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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636 |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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637 ]]> </help> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
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638 <expand macro="citations" /> |
068920e730f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
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639 </tool> |