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comparison consensus.xml @ 19:6cd17fecb4ef draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:57:32 +0000
parents 1e1270416a97
children
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equal deleted inserted replaced
18:b7c4a9147d23 19:6cd17fecb4ef
1 <tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="medaka_consensus" name="medaka inference tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Assembly polishing via neural networks</description> 2 <description> inference from a trained model and alignments.</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"/>
11 ln -s '${bam.metadata.bam_index}' alignment.bam.bai && 11 ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&
12 12
13 ## Possibly new options bam_chunk and bam_workers. Should we be setting these? 13 ## Possibly new options bam_chunk and bam_workers. Should we be setting these?
14 14
15 ## run 15 ## run
16 medaka consensus 16 medaka inference
17 ## optional 17 ## optional
18 --debug ## increase log level 18 --debug ## increase log level
19 --threads \${GALAXY_SLOTS:-4} 19 --threads \${GALAXY_SLOTS:-4}
20 --batch_size $batch_size 20 --batch_size $batch_size
21 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed' 21 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
41 --tag_value $tag_value 41 --tag_value $tag_value
42 #end if 42 #end if
43 $tag_keep_missing 43 $tag_keep_missing
44 ## required 44 ## required
45 alignment.bam ## bam 45 alignment.bam ## bam
46 '$out_result' ## output 46 '$out_result' 2>&1 | tee log.txt
47
48 2>&1 | tee '$out_log'
49 ]]></command> 47 ]]></command>
50 <inputs> 48 <inputs>
51 <param argument="bam" type="data" format="bam" label="Select input alignment"/> 49 <param argument="bam" type="data" format="bam" label="Select input alignment"/>
52 <expand macro="model" argument="--model"/> 50 <expand macro="model" argument="--model"/>
53 <expand macro="b" argument="--batch_size"/> 51 <expand macro="b" argument="--batch_size"/>
82 <!-- standard --> 80 <!-- standard -->
83 <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result"> 81 <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result">
84 <filter>'result' in out</filter> 82 <filter>'result' in out</filter>
85 </data> 83 </data>
86 <!-- optional --> 84 <!-- optional -->
87 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> 85 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
88 <filter>'log' in out</filter> 86 <filter>'log' in out</filter>
89 </data> 87 </data>
90 </outputs> 88 </outputs>
91 <tests> 89 <tests>
92 <!-- #1 default --> 90 <!-- #1 default -->
93 <test expect_num_outputs="1"> 91 <test expect_num_outputs="1">
94 <param name="bam" value="alignment.bam"/> 92 <param name="bam" value="alignment.bam"/>
95 <output name="out_result"> 93 <output name="out_result">
96 <assert_contents> 94 <assert_contents>
97 <has_size value="30960"/> 95 <has_size value="26144"/>
98 </assert_contents> 96 </assert_contents>
99 </output> 97 </output>
100 </test> 98 </test>
101 <!-- #2 --> 99 <!-- #2 -->
102 <test expect_num_outputs="2"> 100 <test expect_num_outputs="2">
103 <param name="bam" value="alignment.bam"/> 101 <param name="bam" value="alignment.bam"/>
104 <param name="model" value="r941_min_fast_g303"/> 102 <param name="model" value="r941_min_fast_g507"/>
105 <param name="batch_size" value="99"/> 103 <param name="batch_size" value="99"/>
106 <param name="chunk_len" value="9999"/> 104 <param name="chunk_len" value="9999"/>
107 <param name="chunk_ovlp" value="999"/> 105 <param name="chunk_ovlp" value="999"/>
108 <param name="check_output" value="true"/> 106 <param name="check_output" value="true"/>
109 <param name="save_features" value="true"/> 107 <param name="save_features" value="true"/>
110 <param name="tag_keep_missing" value="true"/> 108 <param name="tag_keep_missing" value="true"/>
111 <param name="out" value="result,log"/> 109 <param name="out" value="result,log"/>
112 <output name="out_result"> 110 <output name="out_result">
113 <assert_contents> 111 <assert_contents>
114 <has_size value="37088"/> 112 <has_size value="27104"/>
115 </assert_contents> 113 </assert_contents>
116 </output> 114 </output>
117 <output name="out_log"> 115 <output name="out_log">
118 <assert_contents> 116 <assert_contents>
119 <has_text_matching expression=".+Validating and finalising output data."/> 117 <has_text_matching expression=".+Running prediction at full precision"/>
120 </assert_contents> 118 </assert_contents>
121 </output> 119 </output>
122 </test> 120 </test>
123 </tests> 121 </tests>
124 <help><![CDATA[ 122 <help><![CDATA[