Mercurial > repos > iuc > medaka_consensus
comparison consensus.xml @ 2:12c40c8c86db draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
author | iuc |
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date | Thu, 28 May 2020 02:38:54 -0400 |
parents | 0632744d5a5f |
children | 84dcccebad3d |
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1:0632744d5a5f | 2:12c40c8c86db |
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1 <tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 1 <tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
2 <description>Assembly polishing via neural networks</description> | 2 <description>Assembly polishing via neural networks</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="version_command"/> | 7 <expand macro="version_command"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ## initialize | 9 ## initialize |
10 ln -s '${bam}' 'alignment.bam' && | 10 ln -s '${bam}' alignment.bam && |
11 ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' && | 11 ln -s '${bam.metadata.bam_index}' alignment.bam.bai && |
12 | 12 |
13 ## run | 13 ## run |
14 medaka consensus | 14 medaka consensus |
15 ## optional | 15 ## optional |
16 --debug ## increase log level | 16 --debug ## increase log level |
17 --threads \${GALAXY_SLOTS:-4} | 17 --threads \${GALAXY_SLOTS:-4} |
18 --batch_size $batch_size | 18 --batch_size $batch_size |
19 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed' | 19 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed' |
20 --regions | 20 --regions |
21 #if $regions_cond.regions_sel == 'custom' | 21 #if $regions_cond.regions_sel == 'custom' |
22 '$regions_cond.custom' | 22 '$regions_cond.custom' |
23 #else if $regions_cond.regions_sel == 'bed' | 23 #else if $regions_cond.regions_sel == 'bed' |
24 '$regions_cond.bed' | 24 '$regions_cond.bed' |
25 #end if | 25 #end if |
26 #end if | 26 #end if |
27 --chunk_len $chunk_len | 27 --chunk_len $chunk_len |
28 --chunk_ovlp $chunk_ovlp | 28 --chunk_ovlp $chunk_ovlp |
29 --model '$model' | 29 --model $model |
30 $disable_cudnn | 30 $disable_cudnn |
31 $check_output | 31 $check_output |
32 $save_features | 32 $save_features |
33 #if $RG | 33 #if $RG |
34 --RG '$RG' | 34 --RG '$RG' |
35 #end if | 35 #end if |
36 #if $tag_name | 36 #if $tag_name |
37 --tag_name '$tag_name' | 37 --tag_name '$tag_name' |
38 #end if | 38 #end if |
39 #if $tag_value | 39 #if str($tag_value): |
40 --tag_value $tag_value | 40 --tag_value $tag_value |
41 #end if | 41 #end if |
42 $tag_keep_missing | 42 $tag_keep_missing |
43 ## required | 43 ## required |
44 'alignment.bam' ## bam | 44 alignment.bam ## bam |
45 'result.hdf' ## output | 45 '$out_result' ## output |
46 | 46 |
47 |& tee 'log.txt' | 47 |& tee '$out_log' |
48 ]]></command> | 48 ]]></command> |
49 <inputs> | 49 <inputs> |
50 <param argument="bam" type="data" format="bam" label="Select input alignment"/> | 50 <param argument="bam" type="data" format="bam" label="Select input alignment"/> |
51 <expand macro="model" argument="--model"/> | 51 <expand macro="model" argument="--model"/> |
52 <expand macro="b" argument="--batch_size"/> | 52 <expand macro="b" argument="--batch_size"/> |
54 <param name="regions_sel" type="select" label="Specify regions to analyse via"> | 54 <param name="regions_sel" type="select" label="Specify regions to analyse via"> |
55 <option value="none">None</option> | 55 <option value="none">None</option> |
56 <option value="custom">Custom input</option> | 56 <option value="custom">Custom input</option> |
57 <option value="bed">BED file</option> | 57 <option value="bed">BED file</option> |
58 </param> | 58 </param> |
59 <when value="none"/> | |
59 <when value="custom"> | 60 <when value="custom"> |
60 <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/> | 61 <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/> |
61 </when> | 62 </when> |
62 <when value="bed"> | 63 <when value="bed"> |
63 <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/> | 64 <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/> |
64 </when> | 65 </when> |
65 <when value="none"/> | |
66 </conditional> | 66 </conditional> |
67 <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/> | 67 <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/> |
68 <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/> | 68 <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/> |
69 <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/> | 69 <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/> |
70 <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/> | 70 <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/> |
78 <option value="log">Log</option> | 78 <option value="log">Log</option> |
79 </param> | 79 </param> |
80 </inputs> | 80 </inputs> |
81 <outputs> | 81 <outputs> |
82 <!-- standard --> | 82 <!-- standard --> |
83 <data name="out_result" format="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result"> | 83 <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result"> |
84 <filter>'result' in out</filter> | 84 <filter>'result' in out</filter> |
85 </data> | 85 </data> |
86 <!-- optional --> | 86 <!-- optional --> |
87 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"> | 87 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
88 <filter>'log' in out</filter> | 88 <filter>'log' in out</filter> |
89 </data> | 89 </data> |
90 </outputs> | 90 </outputs> |
91 <tests> | 91 <tests> |
92 <!-- #1 default --> | 92 <!-- #1 default --> |