Mercurial > repos > iuc > medaka_consensus

comparison consensus.xml @ 11:0413e62b757a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author iuc
date Thu, 22 Apr 2021 20:24:25 +0000
parents 5901bb391198
children b2aae698b9d3
comparison
equal deleted inserted replaced
10:db25ec99c3ea 11:0413e62b757a
1 <tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy0" 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
13 ## Possibly new options bam_chunk and bam_workers. Should we be setting these?
12 14
13 ## run 15 ## run
14 medaka consensus 16 medaka consensus
15 ## optional 17 ## optional
16 --debug ## increase log level 18 --debug ## increase log level
25 #end if 27 #end if
26 #end if 28 #end if
27 --chunk_len $chunk_len 29 --chunk_len $chunk_len
28 --chunk_ovlp $chunk_ovlp 30 --chunk_ovlp $chunk_ovlp
29 --model $model 31 --model $model
30 $disable_cudnn
31 $check_output 32 $check_output
32 $save_features 33 $save_features
33 #if $RG 34 #if $RG
34 --RG '$RG' 35 --RG '$RG'
35 #end if 36 #end if
64 <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/> 65 <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/>
65 </when> 66 </when>
66 </conditional> 67 </conditional>
67 <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/> 68 <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"/> 69 <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?"/>
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?"/>
71 <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/> 71 <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/>
72 <param argument="--RG" type="text" value="" optional="true" label="Set read group"/> 72 <param argument="--RG" type="text" value="" optional="true" label="Set read group"/>
73 <param argument="--tag_name" type="text" value="" optional="true" label="Set tag name" help="Two letters."/> 73 <param argument="--tag_name" type="text" value="" optional="true" label="Set tag name" help="Two letters."/>
74 <param argument="--tag_value" type="integer" value="" optional="true" label="Set tag value"/> 74 <param argument="--tag_value" type="integer" value="" optional="true" label="Set tag value"/>
103 <param name="bam" value="alignment.bam"/> 103 <param name="bam" value="alignment.bam"/>
104 <param name="model" value="r941_min_fast_g303"/> 104 <param name="model" value="r941_min_fast_g303"/>
105 <param name="batch_size" value="99"/> 105 <param name="batch_size" value="99"/>
106 <param name="chunk_len" value="9999"/> 106 <param name="chunk_len" value="9999"/>
107 <param name="chunk_ovlp" value="999"/> 107 <param name="chunk_ovlp" value="999"/>
108 <param name="disable_cudnn" value="true"/>
109 <param name="check_output" value="true"/> 108 <param name="check_output" value="true"/>
110 <param name="save_features" value="true"/> 109 <param name="save_features" value="true"/>
111 <param name="tag_keep_missing" value="true"/> 110 <param name="tag_keep_missing" value="true"/>
112 <param name="out" value="result,log"/> 111 <param name="out" value="result,log"/>
113 <output name="out_result"> 112 <output name="out_result">