Mercurial > repos > iuc > medaka_variant_pipeline

comparison medaka_variant.xml @ 0:711d4deb7bdf 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 13:37:48 -0400
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-1:000000000000 0:711d4deb7bdf
1 <tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>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 @REF_FASTA@
11 ## link doesn't work
12 cp '${i}' 'alignment.bam' &&
13 cp '${i.metadata.bam_index}' 'alignment.bam.bai' &&
14
15 ## run
16 medaka_variant
17 ## optional
18 #if str($r) != ''
19 -r '$r'
20 #end if
21 -o 'results'
22 -s '$s'
23 -m '$m'
24 -t \${GALAXY_SLOTS:-4}
25 -b $b
26 -N $N
27 -P $P
28 $U
29 $S
30 ## required
31 -i 'alignment.bam'
32 -f 'reference.fa'
33
34 |& tee 'log.txt'
35 ]]></command>
36 <inputs>
37 <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
38 <expand macro="reference"/>
39 <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>
40 <expand macro="model" argument="-s" label="Select model for initial SNP calling from mixed reads prior to phasing"/>
41 <expand macro="model" argument="-m" label="Select model for final variant calling from phased reads"/>
42 <expand macro="b"/>
43 <param argument="-N" type="integer" value="14" label="Set threshold for filtering indels in final VCF"/>
44 <param argument="-P" type="integer" value="12" label="Set threshold for filtering SNPs in final VCF"/>
45 <param argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Avoid filtering of final VCF?"/>
46 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Stop after initial SNP calling from mixed reads prior to phasing?"/>
47 <param name="out" type="select" multiple="true" optional="false" label="Select out file(s)5">
48 <option value="round_0_hap_mixed_phased_bam">round_0_hap_mixed_phased.bam</option>
49 <option value="round_0_hap_mixed_phased_vcf">round_0_hap_mixed_phased.vcf</option>
50 <option value="round_0_hap_mixed_probs_hdf">round_0_hap_mixed_probs.hdf</option>
51 <option value="round_0_hap_mixed_unphased_vcf">round_0_hap_mixed_unphased.vcf</option>
52 <option value="round_1_hap_1_vcf">round_1_hap_1.vcf</option>
53 <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option>
54 <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option>
55 <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option>
56 <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option>
57 <option value="round_1_vcf" selected="true">round_1.vcf</option>
58 <option value="log">Log</option>
59 </param>
60 </inputs>
61 <outputs>
62 <!-- standard -->
63 <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf">
64 <filter>'round_1_vcf' in out</filter>
65 </data>
66 <!-- optional -->
67 <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf">
68 <filter>'round_0_hap_mixed_probs_hdf' in out</filter>
69 </data>
70 <data name="out_round_0_hap_mixed_phased_bam" format="bam" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_bam" from_work_dir="results/round_0_hap_mixed_phased.bam">
71 <filter>'round_0_hap_mixed_phased_bam' in out</filter>
72 </data>
73 <data name="out_round_0_hap_mixed_phased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_vcf" from_work_dir="results/round_0_hap_mixed_phased.vcf">
74 <filter>'round_0_hap_mixed_phased_vcf' in out</filter>
75 </data>
76 <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf">
77 <filter>'round_0_hap_mixed_unphased_vcf' in out</filter>
78 </data>
79 <!-- round 1 -->
80 <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf">
81 <filter>'round_1_hap_1_vcf' in out</filter>
82 </data>
83 <data name="out_round_1_hap_1_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_1_probs.hdf" from_work_dir="results/round_1_hap_1_probs.hdf">
84 <filter>'round_1_hap_1_probs_hdf' in out</filter>
85 </data>
86 <data name="out_round_1_hap_2_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_2.vcf" from_work_dir="results/round_1_hap_2.vcf">
87 <filter>'round_1_hap_2_vcf' in out</filter>
88 </data>
89 <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
90 <filter>'round_1_hap_2_probs_hdf' in out</filter>
91 </data>
92 <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
93 <filter>'round_1_unfiltered_vcf' in out</filter>
94 </data>
95 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
96 <filter>'log' in out</filter>
97 </data>
98 </outputs>
99 <tests>
100 <!-- #1 default -->
101 <test>
102 <param name="i" value="alignment.bam"/>
103 <conditional name="reference_source">
104 <param name="reference_source_selector" value="cached"/>
105 <param name="ref_file" value="bwa-mem-mt-genome"/>
106 </conditional>
107 <param name="out" value="round_0_hap_mixed_probs.hdf,round_0_hap_mixed_unphased.vcf,log"/>
108 <output name="out_round_0_hap_mixed_unphased_vcf">
109 <assert_contents>
110 <has_n_lines n="6"/>
111 <has_line line="##fileformat=VCFv4.1"/>
112 </assert_contents>
113 </output>
114 <output name="out_round_0_hap_mixed_probs_hdf">
115 <assert_contents>
116 <has_size value="32624"/>
117 </assert_contents>
118 </output>
119 <output name="out_log">
120 <assert_contents>
121 <has_line line="++ Preparing data"/>
122 </assert_contents>
123 </output>
124 </test>
125 </tests>
126 <help><![CDATA[
127 .. class:: infomark
128
129 **What it does**
130
131 @WID@
132
133 The module *medaka_variant* performs a variant calling via neural networks.
134
135 **Input**
136
137 It is unlikely that the model arguments should be changed from their defaults.
138
139 - reads aligned to reference (BAM), should be aligned to the reference against which to call variants
140 - reference (FASTA)
141
142 **Output**
143
144 - round_0_hap_mixed_phased.vcf
145 - round_0_hap_mixed_probs.hdf
146 - round_0_hap_mixed_unphased.vcf
147 - round_1_hap_1_probs.hdf
148 - round_1_hap_1.vcf
149 - round_1_hap_2_probs.hdf
150 - round_1_hap_2.vcf
151 - round_1_unfiltered.vcf
152 - round_1.vcf
153
154 **References**
155
156 @REFERENCES@
157 ]]></help>
158 <expand macro="citations"/>
159 </tool>