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comparison consensus.xml @ 1:0632744d5a5f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
author iuc
date Sat, 23 May 2020 13:37:18 -0400
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children 12c40c8c86db
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0:1c4402b9244d 1:0632744d5a5f
1 <tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Assembly polishing via neural networks</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ## initialize
10 ln -s '${bam}' 'alignment.bam' &&
11 ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' &&
12
13 ## run
14 medaka consensus
15 ## optional
16 --debug ## increase log level
17 --threads \${GALAXY_SLOTS:-4}
18 --batch_size $batch_size
19 #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
20 --regions
21 #if $regions_cond.regions_sel == 'custom'
22 '$regions_cond.custom'
23 #else if $regions_cond.regions_sel == 'bed'
24 '$regions_cond.bed'
25 #end if
26 #end if
27 --chunk_len $chunk_len
28 --chunk_ovlp $chunk_ovlp
29 --model '$model'
30 $disable_cudnn
31 $check_output
32 $save_features
33 #if $RG
34 --RG '$RG'
35 #end if
36 #if $tag_name
37 --tag_name '$tag_name'
38 #end if
39 #if $tag_value
40 --tag_value $tag_value
41 #end if
42 $tag_keep_missing
43 ## required
44 'alignment.bam' ## bam
45 'result.hdf' ## output
46
47 |& tee 'log.txt'
48 ]]></command>
49 <inputs>
50 <param argument="bam" type="data" format="bam" label="Select input alignment"/>
51 <expand macro="model" argument="--model"/>
52 <expand macro="b" argument="--batch_size"/>
53 <conditional name="regions_cond">
54 <param name="regions_sel" type="select" label="Specify regions to analyse via">
55 <option value="none">None</option>
56 <option value="custom">Custom input</option>
57 <option value="bed">BED file</option>
58 </param>
59 <when value="custom">
60 <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/>
61 </when>
62 <when value="bed">
63 <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/>
64 </when>
65 <when value="none"/>
66 </conditional>
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"/>
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?"/>
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"/>
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"/>
75 <param argument="--tag_keep_missing" type="boolean" truevalue="--tag_keep_missing" falsevalue="" label="Keep alignments when tag is missing?"/>
76 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
77 <option value="result" selected="true">Result</option>
78 <option value="log">Log</option>
79 </param>
80 </inputs>
81 <outputs>
82 <!-- standard -->
83 <data name="out_result" format="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result">
84 <filter>'result' in out</filter>
85 </data>
86 <!-- optional -->
87 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
88 <filter>'log' in out</filter>
89 </data>
90 </outputs>
91 <tests>
92 <!-- #1 default -->
93 <test expect_num_outputs="1">
94 <param name="bam" value="alignment.bam"/>
95 <output name="out_result">
96 <assert_contents>
97 <has_size value="32624"/>
98 </assert_contents>
99 </output>
100 </test>
101 <!-- #2 -->
102 <test expect_num_outputs="2">
103 <param name="bam" value="alignment.bam"/>
104 <param name="model" value="r941_min_fast_g303"/>
105 <param name="batch_size" value="99"/>
106 <param name="chunk_len" value="9999"/>
107 <param name="chunk_ovlp" value="999"/>
108 <param name="disable_cudnn" value="true"/>
109 <param name="check_output" value="true"/>
110 <param name="save_features" value="true"/>
111 <param name="tag_keep_missing" value="true"/>
112 <param name="out" value="result,log"/>
113 <output name="out_result">
114 <assert_contents>
115 <has_size value="38400"/>
116 </assert_contents>
117 </output>
118 <output name="out_log">
119 <assert_contents>
120 <has_text_matching expression=".+Validating and finalising output data."/>
121 </assert_contents>
122 </output>
123 </test>
124 </tests>
125 <help><![CDATA[
126 .. class:: infomark
127
128 **What it does**
129
130 @WID@
131
132 The module *consensus* runs inference from a trained model and alignments.
133
134 **Input**
135
136 Alignment (BAM)
137
138 **Output**
139
140 Results (H5/HDF)
141
142 **References**
143
144 @REFERENCES@
145 ]]></help>
146 <expand macro="citations"/>
147 </tool>