Mercurial > repos > brinkmanlab > parsnp

annotate ParSNP.xml @ 2:22bf5b566ce2 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit a1f5a7f37fe4e85f7aca1a1476ab30468e1d1578"
author brinkmanlab
date Fri, 13 Mar 2020 14:39:56 -0400
parents 2e855db9b19b
children 2aeddc0a7b0e
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932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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1 <tool id="parsnp" name="ParSNP" version="1.2" profile="16.04">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 <description>Efficient microbial core genome alignment and SNP detection</description>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 <edam_topics>
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4 <edam_topic>topic_3293</edam_topic>
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5 <edam_topic>topic_0194</edam_topic>
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6 <edam_topic>topic_0091</edam_topic>
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7 </edam_topics>
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8 <edam_operations>
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9 <edam_operation>operation_2451</edam_operation>
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10 <edam_operation>operation_0323</edam_operation>
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11 </edam_operations>
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12 <requirements>
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13 <requirement type="package" version="1.2">parsnp</requirement>
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14 </requirements>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 <command detect_errors="aggressive"><![CDATA[
2
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17 export MEMORY_LIMIT=`expr \${GALAXY_MEMORY_MB:-0} \\* 1000`;
22bf5b566ce2 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit a1f5a7f37fe4e85f7aca1a1476ab30468e1d1578"
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18 [[ \$MEMORY_LIMIT -eq 0 ]] && export MEMORY_LIMIT=;
0
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19 export GENOME_DIR=\$(mktemp -d -p `pwd`)
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 #for $genome in $genomes
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21 && ln -sf '$genome'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 #if $adv.use_ids
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23 \$GENOME_DIR/'$genome.element_identifier'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 #else
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25 \$GENOME_DIR/\$(basename '$genome')
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26 #end if
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 #end for
1
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28 && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${MEMORY_LIMIT:-15000000} -d "\$GENOME_DIR"
0
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29 #if $ref_or_gbk.ref_type == "fasta"
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 #if $ref_or_gbk.ref_genome.random_ref
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 -r '!'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32 #else
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 -r '$ref_or_gbk.ref_genome.reference'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 #end if
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 #else
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36 -g '
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 #for $gbk_file in $ref_or_gbk.genbank_files
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 #if $gbk_file
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39 $gbk_file,
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40 #end if
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41 #end for
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42 '
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 #end if
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 $adv.MUMi_or_curated.curated $adv.extend_lcb $adv.output_unaligned
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45 #if $adv.query_genome
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46 -q '$adv.query_genome'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 #end if
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 #unless $adv.MUMi_or_curated.curated
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49 $adv.MUMi_or_curated.MUMi.MUMi_only
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50 #unless $adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution_default
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51 -U '$adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution'
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52 #end unless
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53 #unless $adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance_default
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54 -i '$adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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55 #end unless
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56 #end unless
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57 #unless $adv.min_anchor_len.anchor_default
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58 -a '$adv.min_anchor_len.anchor'
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59 #end unless
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60 -C '$adv.d_value'
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61 -z '$adv.lcb_size'
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62 #if $adv.max_diag_diff.diag_diff_unit
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63 -D '$adv.max_diag_diff.diag_diff_bp$adv.max_diag_diff.diag_diff_unit'
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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64 #else
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65 -D '$adv.max_diag_diff.diag_diff'
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66 #end if
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67 #unless $adv.aligner == "muscle"
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68 -n '$adv.aligner'
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69 #end unless
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70
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71 ]]></command>
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72 <inputs>
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73 <!-- Inputs -->
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74 <param name="genomes" type="data" multiple="true" argument="-d" format="fasta" label="Genomes/Contigs/Scaffolds" />
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75 <conditional name="ref_or_gbk">
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76 <param name="ref_type" type="select" label="Reference type">
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77 <option value="fasta">Single fasta</option>
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78 <option value="gbk">Multiple genbank files</option>
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79 </param>
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80 <when value="fasta">
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81 <conditional name="ref_genome" label="Reference genome">
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82 <param name="random_ref" type="boolean" checked="false" label="Use random genome from above" />
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83 <when value="false">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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84 <param name="reference" type="data" format="fasta" label="Reference"/>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
85 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
86 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
87 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
88 <when value="gbk">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
89 <param name="genbank_files" type="data" format="genbank" argument="-g" multiple="true" label="Reference genbank files" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
90 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
91 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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92
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
93 <section name="adv" title="Advanced options" expanded="false">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
94 <param name="query_genome" type="data" format="fasta" optional="true" label="Specify additional (assembled) query genome to use" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
95 <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" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
96
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
97 <!-- Recombination filtration -->
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
98 <param name="filter_snp" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Enable filtering of SNPs located in PhiPack identified regions of recombination" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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99
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
100 <!-- MUM -->
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
101 <conditional name="min_anchor_len">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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102 <param name="anchor_default" type="boolean" checked="true" label="Minimum ANCHOR length default" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
103 <when value="false">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
104 <param name="anchor" type="float" min="0" value="1.1" label="Minimum ANCHOR length"/>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
105 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
106 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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107 <param name="d_value" type="integer" min="0" value="100" argument="-C" label="Maximal cluster D value"/>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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108 <param name="lcb_size" type="integer" min="0" value="25" argument="-z" label="Min LCB size" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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109
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
110 <!-- MUMi -->
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
111 <conditional name="MUMi_or_curated">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
112 <param name="curated" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Curated genome directory, use all genomes and ignore MUMi" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
113 <when value="">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
114 <conditional name="MUMi">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
115 <param name="MUMi_only" type="boolean" checked="false" truevalue="-M" falsevalue="" argument="-M" label="Only calculate MUMi and exit" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
116 <when value="">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
117 <conditional name="max_mumi_distribution" label="Max MUMi distance value for MUMi distribution">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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118 <param name="max_distribution_default" type="boolean" checked="true" label="Default" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
119 <when value="false">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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120 <param name="max_distribution" type="float" value="1" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
121 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
122 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
123 <conditional name="max_mumi_distance" label="Max MUMi distance">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
124 <param name="max_distance_default" type="boolean" checked="true" label="Autocutoff based on distribution of MUMi values" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
125 <when value="false">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
126 <param name="max_distance" type="float" value="1" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
127 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
128 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
129 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
130 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
131 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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132 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
133
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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134 <!--LCB -->
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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135 <conditional name="max_diag_diff" label="Maximal diagonal difference">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
136 <param name="diag_diff_unit" type="select" label="Unit">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
137 <option value="" selected="true">%</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
138 <option value="bp">Base pairs</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
139 </param>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
140 <when value="">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
141 <param name="diag_diff" type="float" min="0" max="1" value="0.12" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
142 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
143 <when value="bp">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
144 <param name="diag_diff_bp" type="integer" min="0" value="100" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
145 </when>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
146 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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147 <param name="extend_lcb" type="boolean" checked="false" truevalue="-e" falsevalue="" argument="-e" label="Greedily extend LCBs" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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148 <param name="aligner" type="select" argument="-n" label="Alignment program">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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149 <option value="muscle" selected="true">muscle</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
150 <option value="mafft">mafft</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
151 <option value="fsa">fsa</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
152 <option value="prank">prank</option>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
153 </param>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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154 <param name="output_unaligned" type="boolean" checked="false" truevalue="-u" falsevalue="" argument="-u" label="Output unaligned regions" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
155 </section>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
156 </inputs>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
157 <outputs>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
158 <data name="tree" format="newick" from_work_dir="parsnp.tree" label="${tool.name} on ${on_string}: Newick formatted core genome SNP tree" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
159 <data name="vcf" format="vcf" from_work_dir="parsnp.vcf" label="${tool.name} on ${on_string}: SNPs used to infer phylogeny" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
160 <data name="ggr" format="ggr" from_work_dir="parsnp.ggr" label="${tool.name} on ${on_string}: Gingr formatted binary archive" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
161 <data name="xfma" format="xfma" from_work_dir="parsnp.xmfa" label="${tool.name} on ${on_string}: XMFA formatted multiple alignment" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
162 <data name="unaligned" format="txt" from_work_dir="parsnp.unaligned" label="${tool.name} on ${on_string}: Unaligned regions" >
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
163 <filter>adv['output_unaligned']</filter>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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diff changeset
164 </data>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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165 </outputs>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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166 <tests>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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167 <test expect_num_outputs="4">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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168 <param name="genomes" >
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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169 <collection type="list">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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170 <element name="test1" value="test-data/15596_genome.fasta" ftype="fasta" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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171 <element name="test2" value="test-data/15602_genome.fasta" ftype="fasta" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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172 <element name="test3" value="test-data/15599_genome.fasta" ftype="fasta" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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173 </collection>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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174 </param>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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175 <conditional name="ref_or_gbk">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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176 <param name="ref_type" value="fasta" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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177 <conditional name="ref_genome">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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178 <param name="random_ref" value="false" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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179 <param name="reference" value="test-data/15600_genome.fasta" ftype="fasta" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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180 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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181 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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182 <section name="adv">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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183 <conditional name="MUMi_or_curated">
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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184 <param name="curated" value="-c" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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185 </conditional>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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186 </section>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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187 <output name="tree" checksum="sha256:66a2cc47666452fae008b546ab2bd5f9a06c7c7daca88e34e2be7a5cdd371137" ftype="newick" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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188 <output name="vcf" checksum="sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855" ftype="vcf" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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189 <output name="ggr" checksum="sha256:9e91807a25a9549070cfde5cc60844991db5cbee55d9181c61e75220b67f35c5" ftype="txt" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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190 <output name="xfma" checksum="sha256:1774759cc4c34b53e117406a9055f933620960be852ab77501eab1d34badbbfa" ftype="txt" />
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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191 </test>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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192 </tests>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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193 <help><![CDATA[
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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194 https://harvest.readthedocs.io/en/latest/content/parsnp.html
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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195 ]]></help>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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196 <citations>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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197 <citation type="doi">10.5281/zenodo.3364789</citation>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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198 <citation type="doi">10.1101/007351</citation>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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199 </citations>
932410434dd1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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200 </tool>