Mercurial > repos > jowong > khmer_load_into_counting
comparison khmer_load_into_counting.xml @ 1:f491d18251e9 draft
planemo upload
| author | jowong |
|---|---|
| date | Mon, 26 Nov 2018 02:14:27 -0500 |
| parents | 69d52f45c2fa |
| children | ab0f91be3a90 |
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| 0:69d52f45c2fa | 1:f491d18251e9 |
|---|---|
| 1 <tool id="khmer_load_into_counting" name="Load Into Counting" version="0.1.5"> | 1 <tool id="khmer_load_into_counting" name="Load Into Counting" version="1.0.5"> |
| 2 <description>Creates k-mer countgraph using reads</description> | 2 <description>Creates k-mer countgraph using reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.1.2">khmer</requirement> | 4 <requirement type="package" version="2.1.2">khmer</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 load-into-counting.py | 7 load-into-counting.py |
| 8 $advanced.b | 8 $advanced.b |
| 9 $advanced.small | 9 $advanced.small |
| 10 -k $advanced.kmer | 10 -k $kmer |
| 11 -U $advanced.ukmer | 11 -U $advanced.ukmer |
| 12 #if str( $advanced.max_mem ) != "0" | 12 #if str( $advanced.max_mem ) != "0" |
| 13 -M $advanced.max_mem | 13 -M $advanced.max_mem |
| 14 #end if | 14 #end if |
| 15 #if str( $advanced.fp_rate ) != "0" | 15 #if str( $advanced.fp_rate ) != "0" |
| 16 --fp-rate $advanced.fp_rate | 16 --fp-rate $advanced.fp_rate |
| 17 #end if | 17 #end if |
| 18 #if str( $advanced.num_table ) != "0" | 18 -N $advanced.num_table |
| 19 -N $advanced.num_table | 19 -x $advanced.table_size |
| 20 #end if | |
| 21 #if str( $advanced.table_size ) != "0" | |
| 22 -x $advanced.table_size | |
| 23 #end if | |
| 24 hash.ct.gz | 20 hash.ct.gz |
| 25 #if str( $data_input.data_selector ) == "paired" | 21 #if str( $data_input.data_selector ) == "paired" |
| 26 $data_input.input1.forward $data_input.input1.reverse | 22 $data_input.input1.forward $data_input.input1.reverse |
| 27 #end if | 23 #end if |
| 28 #if str( $data_input.data_selector ) == "single" | 24 #if str( $data_input.data_selector ) == "single" |
| 40 </when> | 36 </when> |
| 41 <when value="single"> | 37 <when value="single"> |
| 42 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> | 38 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> |
| 43 </when> | 39 </when> |
| 44 </conditional> | 40 </conditional> |
| 41 <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" /> | |
| 45 <section name="advanced" title="Advanced options" expanded="false"> | 42 <section name="advanced" title="Advanced options" expanded="false"> |
| 46 <param type="boolean" argument="--small" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/> | 43 <param type="boolean" argument="--small" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/> |
| 47 <param type="boolean" argument="-b" label="big count" checked="True" truevalue="-b" falsevalue="--no-bigcount" help="Reduce memory usage by using a smaller counter for individual kmers. (default: True)"/> | 44 <param type="boolean" argument="-b" label="big count" checked="True" truevalue="-b" falsevalue="--no-bigcount" help="Reduce memory usage by using a smaller counter for individual kmers. (default: True)"/> |
| 48 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" /> | 45 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" /> |
| 49 <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" /> | 46 |
| 50 <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" /> | 47 <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" /> |
| 51 <param name="num_table" type="integer" value="0" label="Number of tables" help="number of tables to use (default: False)" /> | 48 <param name="num_table" type="integer" value="1" label="Number of tables" help="number of tables to use (default: False)" /> |
| 52 <param name="table_size" type="integer" value="0" label="Maximum size of table" help="maximum size of tables to use (default: False)" /> | 49 <param name="table_size" type="integer" value="1000000000" label="Maximum size of table" help="maximum size of tables to use (default: False)" /> |
| 53 <param name="max_mem" type="integer" value="0" label="Maximum Memory" help="number of tables to use (default: False)" /> | 50 <param name="max_mem" type="integer" value="0" label="Maximum Memory" help="number of tables to use (default: False)" /> |
| 54 <param name="fp_rate" type="integer" value="0" label="FP rate override" help="Override the automatic FP rate setting for the current script" /> | 51 <param name="fp_rate" type="integer" value="0" label="FP rate override" help="Override the automatic FP rate setting for the current script" /> |
| 55 </section> | 52 </section> |
| 56 </inputs> | 53 </inputs> |
| 57 <outputs> | 54 <outputs> |