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comparison ParSNP.xml @ 0:932410434dd1 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:45:42 -0500
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children 2e855db9b19b
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-1:000000000000 0:932410434dd1
1 <tool id="parsnp" name="ParSNP" version="1.2" profile="16.04">
2 <description>Efficient microbial core genome alignment and SNP detection</description>
3 <edam_topics>
4 <edam_topic>topic_3293</edam_topic>
5 <edam_topic>topic_0194</edam_topic>
6 <edam_topic>topic_0091</edam_topic>
7 </edam_topics>
8 <edam_operations>
9 <edam_operation>operation_2451</edam_operation>
10 <edam_operation>operation_0323</edam_operation>
11 </edam_operations>
12 <requirements>
13 <requirement type="package" version="1.2">parsnp</requirement>
14 </requirements>
15 <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command>
16 <command detect_errors="aggressive"><![CDATA[
17 export GENOME_DIR=\$(mktemp -d -p `pwd`)
18 #for $genome in $genomes
19 && ln -sf '$genome'
20 #if $adv.use_ids
21 \$GENOME_DIR/'$genome.element_identifier'
22 #else
23 \$GENOME_DIR/\$(basename '$genome')
24 #end if
25 #end for
26 && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${GALAXY_MEMORY_MB:-15000000} -d "\$GENOME_DIR"
27 #if $ref_or_gbk.ref_type == "fasta"
28 #if $ref_or_gbk.ref_genome.random_ref
29 -r '!'
30 #else
31 -r '$ref_or_gbk.ref_genome.reference'
32 #end if
33 #else
34 -g '
35 #for $gbk_file in $ref_or_gbk.genbank_files
36 #if $gbk_file
37 $gbk_file,
38 #end if
39 #end for
40 '
41 #end if
42 $adv.MUMi_or_curated.curated $adv.extend_lcb $adv.output_unaligned
43 #if $adv.query_genome
44 -q '$adv.query_genome'
45 #end if
46 #unless $adv.MUMi_or_curated.curated
47 $adv.MUMi_or_curated.MUMi.MUMi_only
48 #unless $adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution_default
49 -U '$adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution'
50 #end unless
51 #unless $adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance_default
52 -i '$adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance'
53 #end unless
54 #end unless
55 #unless $adv.min_anchor_len.anchor_default
56 -a '$adv.min_anchor_len.anchor'
57 #end unless
58 -C '$adv.d_value'
59 -z '$adv.lcb_size'
60 #if $adv.max_diag_diff.diag_diff_unit
61 -D '$adv.max_diag_diff.diag_diff_bp$adv.max_diag_diff.diag_diff_unit'
62 #else
63 -D '$adv.max_diag_diff.diag_diff'
64 #end if
65 #unless $adv.aligner == "muscle"
66 -n '$adv.aligner'
67 #end unless
68
69 ]]></command>
70 <inputs>
71 <!-- Inputs -->
72 <param name="genomes" type="data" multiple="true" argument="-d" format="fasta" label="Genomes/Contigs/Scaffolds" />
73 <conditional name="ref_or_gbk">
74 <param name="ref_type" type="select" label="Reference type">
75 <option value="fasta">Single fasta</option>
76 <option value="gbk">Multiple genbank files</option>
77 </param>
78 <when value="fasta">
79 <conditional name="ref_genome" label="Reference genome">
80 <param name="random_ref" type="boolean" checked="false" label="Use random genome from above" />
81 <when value="false">
82 <param name="reference" type="data" format="fasta" label="Reference"/>
83 </when>
84 </conditional>
85 </when>
86 <when value="gbk">
87 <param name="genbank_files" type="data" format="genbank" argument="-g" multiple="true" label="Reference genbank files" />
88 </when>
89 </conditional>
90
91 <section name="adv" title="Advanced options" expanded="false">
92 <param name="query_genome" type="data" format="fasta" optional="true" label="Specify additional (assembled) query genome to use" />
93 <param name="use_ids" type="boolean" checked="true" label="Use dataset name or collection id's instead of file name in output" help="IDs must be valid POSIX file names" />
94
95 <!-- Recombination filtration -->
96 <param name="filter_snp" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Enable filtering of SNPs located in PhiPack identified regions of recombination" />
97
98 <!-- MUM -->
99 <conditional name="min_anchor_len">
100 <param name="anchor_default" type="boolean" checked="true" label="Minimum ANCHOR length default" />
101 <when value="false">
102 <param name="anchor" type="float" min="0" value="1.1" label="Minimum ANCHOR length"/>
103 </when>
104 </conditional>
105 <param name="d_value" type="integer" min="0" value="100" argument="-C" label="Maximal cluster D value"/>
106 <param name="lcb_size" type="integer" min="0" value="25" argument="-z" label="Min LCB size" />
107
108 <!-- MUMi -->
109 <conditional name="MUMi_or_curated">
110 <param name="curated" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Curated genome directory, use all genomes and ignore MUMi" />
111 <when value="">
112 <conditional name="MUMi">
113 <param name="MUMi_only" type="boolean" checked="false" truevalue="-M" falsevalue="" argument="-M" label="Only calculate MUMi and exit" />
114 <when value="">
115 <conditional name="max_mumi_distribution" label="Max MUMi distance value for MUMi distribution">
116 <param name="max_distribution_default" type="boolean" checked="true" label="Default" />
117 <when value="false">
118 <param name="max_distribution" type="float" value="1" />
119 </when>
120 </conditional>
121 <conditional name="max_mumi_distance" label="Max MUMi distance">
122 <param name="max_distance_default" type="boolean" checked="true" label="Autocutoff based on distribution of MUMi values" />
123 <when value="false">
124 <param name="max_distance" type="float" value="1" />
125 </when>
126 </conditional>
127 </when>
128 </conditional>
129 </when>
130 </conditional>
131
132 <!--LCB -->
133 <conditional name="max_diag_diff" label="Maximal diagonal difference">
134 <param name="diag_diff_unit" type="select" label="Unit">
135 <option value="" selected="true">%</option>
136 <option value="bp">Base pairs</option>
137 </param>
138 <when value="">
139 <param name="diag_diff" type="float" min="0" max="1" value="0.12" />
140 </when>
141 <when value="bp">
142 <param name="diag_diff_bp" type="integer" min="0" value="100" />
143 </when>
144 </conditional>
145 <param name="extend_lcb" type="boolean" checked="false" truevalue="-e" falsevalue="" argument="-e" label="Greedily extend LCBs" />
146 <param name="aligner" type="select" argument="-n" label="Alignment program">
147 <option value="muscle" selected="true">muscle</option>
148 <option value="mafft">mafft</option>
149 <option value="fsa">fsa</option>
150 <option value="prank">prank</option>
151 </param>
152 <param name="output_unaligned" type="boolean" checked="false" truevalue="-u" falsevalue="" argument="-u" label="Output unaligned regions" />
153 </section>
154 </inputs>
155 <outputs>
156 <data name="tree" format="newick" from_work_dir="parsnp.tree" label="${tool.name} on ${on_string}: Newick formatted core genome SNP tree" />
157 <data name="vcf" format="vcf" from_work_dir="parsnp.vcf" label="${tool.name} on ${on_string}: SNPs used to infer phylogeny" />
158 <data name="ggr" format="ggr" from_work_dir="parsnp.ggr" label="${tool.name} on ${on_string}: Gingr formatted binary archive" />
159 <data name="xfma" format="xfma" from_work_dir="parsnp.xmfa" label="${tool.name} on ${on_string}: XMFA formatted multiple alignment" />
160 <data name="unaligned" format="txt" from_work_dir="parsnp.unaligned" label="${tool.name} on ${on_string}: Unaligned regions" >
161 <filter>adv['output_unaligned']</filter>
162 </data>
163 </outputs>
164 <tests>
165 <test expect_num_outputs="4">
166 <param name="genomes" >
167 <collection type="list">
168 <element name="test1" value="test-data/15596_genome.fasta" ftype="fasta" />
169 <element name="test2" value="test-data/15602_genome.fasta" ftype="fasta" />
170 <element name="test3" value="test-data/15599_genome.fasta" ftype="fasta" />
171 </collection>
172 </param>
173 <conditional name="ref_or_gbk">
174 <param name="ref_type" value="fasta" />
175 <conditional name="ref_genome">
176 <param name="random_ref" value="false" />
177 <param name="reference" value="test-data/15600_genome.fasta" ftype="fasta" />
178 </conditional>
179 </conditional>
180 <section name="adv">
181 <conditional name="MUMi_or_curated">
182 <param name="curated" value="-c" />
183 </conditional>
184 </section>
185 <output name="tree" checksum="sha256:66a2cc47666452fae008b546ab2bd5f9a06c7c7daca88e34e2be7a5cdd371137" ftype="newick" />
186 <output name="vcf" checksum="sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855" ftype="vcf" />
187 <output name="ggr" checksum="sha256:9e91807a25a9549070cfde5cc60844991db5cbee55d9181c61e75220b67f35c5" ftype="txt" />
188 <output name="xfma" checksum="sha256:1774759cc4c34b53e117406a9055f933620960be852ab77501eab1d34badbbfa" ftype="txt" />
189 </test>
190 </tests>
191 <help><![CDATA[
192 https://harvest.readthedocs.io/en/latest/content/parsnp.html
193 ]]></help>
194 <citations>
195 <citation type="doi">10.5281/zenodo.3364789</citation>
196 <citation type="doi">10.1101/007351</citation>
197 </citations>
198 </tool>