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comparison microsatbed.xml @ 1:1a0ea94317a9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 0c8ab2d9c2783fdc33d3eac057f2a29e298d7264
author iuc
date Wed, 14 Aug 2024 08:49:28 +0000
parents dee16d45a2a9
children e2ae68224857
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0:dee16d45a2a9 1:1a0ea94317a9
1 1
2 <tool id="microsatbed" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> 2 <tool id="microsatbed" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
3 <description>Short Tandem Repeats to bed features from fasta</description> 3 <description>Short Tandem Repeats to bed features from fasta</description>
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">1.3.2</token> 5 <token name="@TOOL_VERSION@">1.3.2</token>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">1</token>
7 <token name="@PYFASTX_VERSION@">2.1.0</token>
8 <token name="@PYTHON_VERSION@">3.12.3</token> 7 <token name="@PYTHON_VERSION@">3.12.3</token>
9 <token name="@UCSC_VERSION@">455</token>
10 <macro name="subsetmacro"> 8 <macro name="subsetmacro">
11 <param name="subset" type="select" label="Select at least 1 specific motif length to report" help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more" multiple="true"> 9 <param name="subset" type="select" label="Select at least 1 specific motif length to report"
10 help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more" multiple="true">
12 <option value="--di" selected="true">All dimers (AC,AG,AT,...)</option> 11 <option value="--di" selected="true">All dimers (AC,AG,AT,...)</option>
13 <option value="--tri">All trimers (ACG,..)</option> 12 <option value="--tri">All trimers (ACG,..)</option>
14 <option value="--tetra">All tetramers (ACGT,..)</option> 13 <option value="--tetra">All tetramers (ACGT,..)</option>
15 <option value="--penta">All pentamers (ACGTC,..)</option> 14 <option value="--penta">All pentamers (ACGTC,..)</option>
16 <option value="--hexa">All hexamers (ACGTCG,..)</option> 15 <option value="--hexa">All hexamers (ACGTCG,..)</option>
18 </param> 17 </param>
19 </macro> 18 </macro>
20 </macros> 19 </macros>
21 <requirements> 20 <requirements>
22 <requirement version="@PYTHON_VERSION@" type="package">python</requirement> 21 <requirement version="@PYTHON_VERSION@" type="package">python</requirement>
23 <requirement version="@PYFASTX_VERSION@" type="package">pyfastx</requirement> 22 <requirement version="2.1.0" type="package">pyfastx</requirement>
24 <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement> 23 <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement>
25 <requirement version="@UCSC_VERSION@" type="package">ucsc-bedgraphtobigwig</requirement> 24 <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
26 </requirements> 25 </requirements>
27 <required_files> 26 <required_files>
28 <include path="find_str.py"/> 27 <include path="find_str.py"/>
29 </required_files> 28 </required_files>
30 <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command> 29 <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
31 <command><![CDATA[ 30 <command><![CDATA[
32 #if $mode_cond.mode == "NATIVE": 31 #if $mode_cond.mode == "NATIVE":
33 #if $reference_genome.genome_type_select == "history": 32 #if str($reference_genome.genome_type_select) == "history":
34 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta}' 33 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.reffa}'
35 #else: 34 #else:
36 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta.fields.path}' 35 pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.reffa.fields.path}'
37 #end if 36 #end if
38 #else: 37 #else:
39 python '${__tool_directory__}/find_str.py' 38 python '${__tool_directory__}/find_str.py'
40 #if $reference_genome.genome_type_select == "history": 39 #if str($reference_genome.genome_type_select) == "history":
41 --fasta '${reference_genome.fasta}' 40 --fasta '${reference_genome.reffa}'
42 #else: 41 #else:
43 --fasta '${reference_genome.fasta.fields.path}' 42 --fasta '${reference_genome.reffa.fields.path}'
44 #end if 43 #end if
45 --bed '$bed' 44 --bed '$bed'
46 #if $mode_cond.mode == "SPECIFIC": 45 #if $mode_cond.mode == "SPECIFIC":
47 --specific '$mode_cond.specific' 46 --specific '$mode_cond.specific'
48 #elif $mode_cond.mode == "SPECIFICBW": 47 #elif $mode_cond.mode == "SPECIFICBW":
71 <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file"> 70 <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
72 <option value="indexed">Use a Galaxy server built-in reference genome fasta</option> 71 <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
73 <option value="history" selected="True">Use any fasta file from the current history</option> 72 <option value="history" selected="True">Use any fasta file from the current history</option>
74 </param> 73 </param>
75 <when value="indexed"> 74 <when value="indexed">
76 <param name="fasta" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" > 75 <param name="reffa" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
77 <options from_data_table="all_fasta"/> 76 <options from_data_table="all_fasta"/>
78 </param> 77 </param>
79 </when> 78 </when>
80 <when value="history"> 79 <when value="history">
81 <param name="fasta" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" /> 80 <param name="reffa" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
82 </when> 81 </when>
83 </conditional> 82 </conditional>
84 <conditional name="mode_cond"> 83 <conditional name="mode_cond">
85 <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode"> 84 <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
86 <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option> 85 <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>
117 <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/> 116 <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
118 <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/> 117 <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
119 <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/> 118 <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
120 </inputs> 119 </inputs>
121 <outputs> 120 <outputs>
122 <data name="bed" format="bed" label="STR from $fasta.element_identifier"> 121 <data name="bed" format="bed" label="STR in ${on_string}">
123 <change_format> 122 <change_format>
124 <when input="mode_cond.outformat" value="gff" format="gff"/> 123 <when input="mode_cond.outformat" value="gff" format="gff"/>
125 <when input="mode_cond.outformat" value="csv" format="csv"/> 124 <when input="mode_cond.outformat" value="csv" format="csv"/>
126 <when input="mode_cond.outformat" value="tsv" format="tabular"/> 125 <when input="mode_cond.outformat" value="tsv" format="tabular"/>
127 <when input="mode_cond.mode" value="ALLBW" format="bigwig"/> 126 <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>
131 </outputs> 130 </outputs>
132 <tests> 131 <tests>
133 <test expect_num_outputs="1"> 132 <test expect_num_outputs="1">
134 <conditional name="reference_genome"> 133 <conditional name="reference_genome">
135 <param name="genome_type_select" value="history"/> 134 <param name="genome_type_select" value="history"/>
136 <param name="fasta" value="humsamp.fa"/> 135 <param name="reffa" value="humsamp.fa"/>
137 </conditional> 136 </conditional>
138 <conditional name="mode_cond"> 137 <conditional name="mode_cond">
139 <param name="mode" value="ALL"/> 138 <param name="mode" value="ALL"/>
140 <param name="subset" value="--di,--tri,--tetra,--penta,--hexa"/> 139 <param name="subset" value="--di,--tri,--tetra,--penta,--hexa"/>
141 </conditional> 140 </conditional>
155 </output> 154 </output>
156 </test> 155 </test>
157 <test expect_num_outputs="1"> 156 <test expect_num_outputs="1">
158 <conditional name="reference_genome"> 157 <conditional name="reference_genome">
159 <param name="genome_type_select" value="history"/> 158 <param name="genome_type_select" value="history"/>
160 <param name="fasta" value="humsamp.fa"/> 159 <param name="reffa" value="humsamp.fa"/>
161 </conditional> 160 </conditional>
162 <conditional name="mode_cond"> 161 <conditional name="mode_cond">
163 <param name="mode" value="SPECIFIC"/> 162 <param name="mode" value="SPECIFIC"/>
164 <param name="specific" value="GC"/> 163 <param name="specific" value="GC"/>
165 </conditional> 164 </conditional>
180 </output> 179 </output>
181 </test> 180 </test>
182 <test expect_num_outputs="1"> 181 <test expect_num_outputs="1">
183 <conditional name="reference_genome"> 182 <conditional name="reference_genome">
184 <param name="genome_type_select" value="history"/> 183 <param name="genome_type_select" value="history"/>
185 <param name="fasta" value="mouse.fa"/> 184 <param name="reffa" value="mouse.fa"/>
186 </conditional> 185 </conditional>
187 <conditional name="mode_cond"> 186 <conditional name="mode_cond">
188 <param name="mode" value="NATIVE"/> 187 <param name="mode" value="NATIVE"/>
189 <param name="outformat" value="gff"/> 188 <param name="outformat" value="gff"/>
190 </conditional> 189 </conditional>
203 </assert_contents> 202 </assert_contents>
204 </output> 203 </output>
205 </test> 204 </test>
206 <test expect_num_outputs="1"> 205 <test expect_num_outputs="1">
207 <conditional name="reference_genome"> 206 <conditional name="reference_genome">
208 <param name="genome_type_select" value="history"/> 207 <param name="genome_type_select" value="indexed"/>
209 <param name="fasta" value="humsamp.fa"/> 208 <param name="reffa" value="hgtest"/>
210 </conditional> 209 </conditional>
211 <conditional name="mode_cond"> 210 <conditional name="mode_cond">
212 <param name="mode" value="SPECIFICBW"/> 211 <param name="mode" value="SPECIFICBW"/>
213 <param name="specific" value="GC"/> 212 <param name="specific" value="GC"/>
214 </conditional> 213 </conditional>