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comparison microsatbed.xml @ 17:264d79548d19 draft

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planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
author fubar
date Wed, 17 Jul 2024 06:08:33 +0000
parents ee773bbde3c3
children 607620f93b4c
comparison
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16:ee773bbde3c3 17:264d79548d19
10 </required_files> 10 </required_files>
11 <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command> 11 <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
12 <command><![CDATA[ 12 <command><![CDATA[
13 #if $mode_cond.mode == "NATIVE": 13 #if $mode_cond.mode == "NATIVE":
14 #if $reference_genome.genome_type_select == "history": 14 #if $reference_genome.genome_type_select == "history":
15 pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}' 15 pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta}'
16 #else: 16 #else:
17 pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta.fields.path}' 17 pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta.fields.path}'
18 #end if 18 #end if
19 #else: 19 #else:
20 python '${__tool_directory__}/find_str.py' 20 python '${__tool_directory__}/find_str.py'
21 #if $reference_genome.genome_type_select == "history": 21 #if $reference_genome.genome_type_select == "history":
22 --fasta '${reference_genome.fasta}' 22 --fasta '${reference_genome.fasta}'
24 --fasta '${reference_genome.fasta.fields.path}' 24 --fasta '${reference_genome.fasta.fields.path}'
25 #end if 25 #end if
26 --bed '$bed' 26 --bed '$bed'
27 #if $mode_cond.mode == "SPECIFIC": 27 #if $mode_cond.mode == "SPECIFIC":
28 --specific '$mode_cond.specific' 28 --specific '$mode_cond.specific'
29 --minreps '$mode_cond.minreps' 29 --monomin '$monomin'
30 --dimin '$dimin'
31 --trimin '$trimin'
32 --tetramin '$tetramin'
33 --pentamin '$pentamin'
34 --hexamin '$hexamin'
30 #else: 35 #else:
31 #if "MONO" in $mode_cond.subset: 36 #if "MONO" in $mode_cond.subset:
32 --mono 37 --mono
33 #end if 38 #end if
34 #if "DI" in $mode_cond.subset: 39 #if "DI" in $mode_cond.subset:
44 --penta 49 --penta
45 #end if 50 #end if
46 #if "HEXA" in $mode_cond.subset: 51 #if "HEXA" in $mode_cond.subset:
47 --hexa 52 --hexa
48 #end if 53 #end if
49 --monomin '$mode_cond.monomin' 54 --monomin '$monomin'
50 --dimin '$mode_cond.dimin' 55 --dimin '$dimin'
51 --trimin '$mode_cond.trimin' 56 --trimin '$trimin'
52 --tetramin '$mode_cond.tetramin' 57 --tetramin '$tetramin'
53 --pentamin '$mode_cond.pentamin' 58 --pentamin '$pentamin'
54 --hexamin '$mode_cond.hexamin' 59 --hexamin '$hexamin'
55 #end if 60 #end if
56 #end if 61 #end if
57 ]]></command> 62 ]]></command>
58 <inputs> 63 <inputs>
59 <conditional name="reference_genome"> 64 <conditional name="reference_genome">
78 <option value="NATIVE">All exact STR: use the pytrf findstr native command to a create csv, tsv or gtf output</option> 83 <option value="NATIVE">All exact STR: use the pytrf findstr native command to a create csv, tsv or gtf output</option>
79 </param> 84 </param>
80 <when value="ALL"> 85 <when value="ALL">
81 <param name="subset" type="select" multiple="true" optional="false" label="Select at least 1 specific motif length to report" 86 <param name="subset" type="select" multiple="true" optional="false" label="Select at least 1 specific motif length to report"
82 help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more"> 87 help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more">
83 <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option> 88 <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option>
84 <option value="TRI">All trimers (ACG,..)</option> 89 <option value="TRI">All trimers (ACG,..)</option>
85 <option value="TETRA">All tetramers (ACGT,..)</option> 90 <option value="TETRA">All tetramers (ACGT,..)</option>
86 <option value="PENTA">All pentamers (ACGTC,..)</option> 91 <option value="PENTA">All pentamers (ACGTC,..)</option>
87 <option value="HEXA">All hexamers (ACGTCG,..)</option> 92 <option value="HEXA">All hexamers (ACGTCG,..)</option>
88 <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option> 93 <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option>
89 </param> 94 </param>
90 <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/>
91 <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/>
92 <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/>
93 <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/>
94 <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/>
95 <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
96 </when> 95 </when>
97 <when value="SPECIFIC"> 96 <when value="SPECIFIC">
98 <param name="specific" type="text" label="Supply a specific motif pattern. Separate multiple patterns with commas such as GA,GC" 97 <param name="specific" type="text" label="Supply a specific motif pattern. Separate multiple patterns with commas such as GA,GC"
99 help="Make bed features only for the nominated specific motifs." optional="false"/> 98 help="Make bed features only for the nominated specific motifs." optional="false"/>
100 <param name="minreps" type="integer" value="2" min="1" label="Minimum number of repeats of each of these motifs to report"
101 help="Short tandem repeats require 2 or more consecutive motifs by definition. WARNING: If monomers are included, every single matching base will be reported as a STR if minimum repeats = 1!"
102 optional="false"/>
103 </when> 99 </when>
104 <when value="NATIVE"> 100 <when value="NATIVE">
105 <param name="outformat" type="select" optional="false" label="Select the required output format" 101 <param name="outformat" type="select" optional="false" label="Select the required output format"
106 help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below"> 102 help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below">
107 <option value="gff" >GFF</option> 103 <option value="gff" >GFF</option>
108 <option value="csv">Comma separated values</option> 104 <option value="csv">Comma separated values</option>
109 <option value="tsv" selected="true">Tab separated values</option> 105 <option value="tsv" selected="true">Tab separated values</option>
110 </param> 106 </param>
111 <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
112 <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/>
113 <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/>
114 <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/>
115 <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/>
116 <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/>
117 </when> 107 </when>
118 </conditional> 108 </conditional>
109 <param type="integer" min="2" name="monomin" value="10"/>
110 <param type="integer" min="1" name="dimin" value="3"/>
111 <param type="integer" min="2" name="trimin" value="2"/>
112 <param type="integer" min="2" name="tetramin" value="2"/>
113 <param type="integer" min="2" name="pentamin" value="2"/>
114 <param type="integer" min="2" name="hexamin" value="2"/>
119 </inputs> 115 </inputs>
120 <outputs> 116 <outputs>
121 <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false"> 117 <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">
122 <change_format> 118 <change_format>
123 <when input="mode_cond.outformat" value="gff" format="gff" /> 119 <when input="mode_cond.outformat" value="gff" format="gff" />
133 <param name="fasta" value="humsamp.fa"/> 129 <param name="fasta" value="humsamp.fa"/>
134 </conditional> 130 </conditional>
135 <conditional name="mode_cond"> 131 <conditional name="mode_cond">
136 <param name="mode" value="ALL"/> 132 <param name="mode" value="ALL"/>
137 <param name="subset" value="DI,TRI,TETRA,PENTA,HEXA"/> 133 <param name="subset" value="DI,TRI,TETRA,PENTA,HEXA"/>
138 <param name="dimin" value="2"/> 134 </conditional>
139 <param name="trimin" value="2"/> 135 <param name="monomin" value="20"/>
140 <param name="tetramin" value="2"/> 136 <param name="dimin" value="2"/>
141 <param name="pentamin" value="2"/> 137 <param name="trimin" value="2"/>
142 <param name="hexamin" value="2"/> 138 <param name="tetramin" value="2"/>
143 </conditional> 139 <param name="pentamin" value="2"/>
140 <param name="hexamin" value="2"/>
144 <output name="bed" value="bed_sample" compare="diff" lines_diff="0"/> 141 <output name="bed" value="bed_sample" compare="diff" lines_diff="0"/>
145 </test> 142 </test>
146 <test expect_num_outputs="1"> 143 <test expect_num_outputs="1">
147 <conditional name="reference_genome"> 144 <conditional name="reference_genome">
148 <param name="genome_type_select" value="history"/> 145 <param name="genome_type_select" value="history"/>
149 <param name="fasta" value="humsamp.fa"/> 146 <param name="fasta" value="humsamp.fa"/>
150 </conditional> 147 </conditional>
151 <conditional name="mode_cond"> 148 <conditional name="mode_cond">
152 <param name="mode" value="SPECIFIC"/> 149 <param name="mode" value="SPECIFIC"/>
153 <param name="specific" value="GC"/> 150 <param name="specific" value="GC"/>
154 <param name="minreps" value="2"/> 151 </conditional>
155 </conditional> 152 <param name="monomin" value="20"/>
153 <param name="dimin" value="1"/>
154 <param name="trimin" value="20"/>
155 <param name="tetramin" value="20"/>
156 <param name="pentamin" value="20"/>
157 <param name="hexamin" value="20"/>
156 <output name="bed" value="dibed_sample" compare="diff" lines_diff="0"/> 158 <output name="bed" value="dibed_sample" compare="diff" lines_diff="0"/>
157 </test> 159 </test>
158 <test expect_num_outputs="1"> 160 <test expect_num_outputs="1">
159 <conditional name="reference_genome"> 161 <conditional name="reference_genome">
160 <param name="genome_type_select" value="history"/> 162 <param name="genome_type_select" value="history"/>
161 <param name="fasta" value="mouse.fa"/> 163 <param name="fasta" value="mouse.fa"/>
162 </conditional> 164 </conditional>
163 <conditional name="mode_cond"> 165 <conditional name="mode_cond">
164 <param name="mode" value="NATIVE"/> 166 <param name="mode" value="NATIVE"/>
165 <param name="outformat" value="gff"/> 167 <param name="outformat" value="gff"/>
166 <param name="monomin" value="20"/> 168 </conditional>
167 <param name="dimin" value="10"/> 169 <param name="monomin" value="20"/>
168 <param name="trimin" value="5"/> 170 <param name="dimin" value="10"/>
169 <param name="tetramin" value="4"/> 171 <param name="trimin" value="5"/>
170 <param name="pentamin" value="4"/> 172 <param name="tetramin" value="4"/>
171 <param name="hexamin" value="2"/> 173 <param name="pentamin" value="4"/>
172 </conditional> 174 <param name="hexamin" value="2"/>
173 <output name="bed" value="nativegff_sample" compare="diff" lines_diff="0"/> 175 <output name="bed" value="nativegff_sample" compare="diff" lines_diff="0"/>
174 </test> 176 </test>
175 </tests> 177 </tests>
176 <help><![CDATA[ 178 <help><![CDATA[
177 179