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comparison gfastats.xml @ 8:6ec1b853c8fd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 53b8f235e87107323cc6e636cc0d069551a44dec
author bgruening
date Thu, 10 Oct 2024 09:58:15 +0000
parents 3ef480892a9f
children
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7:3ef480892a9f 8:6ec1b853c8fd
1 <tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> 1 <tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2">
2 <description>the swiss army knife for genome assembly</description> 2 <description>The swiss army knife for Genome Assembly</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="biotools"/> 6 <expand macro="biotools"/>
7 <expand macro="requirements"/>
8 <version_command>gfastats --version</version_command> 8 <version_command>gfastats --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 gfastats 10 gfastats
11 '$input_file' 11 '$input_file'
12 #if $mode_condition.selector == 'statistics' 12 #if $mode_condition.selector == 'statistics'
32 #end if 32 #end if
33 #if $mode_condition.homopolymer_compress 33 #if $mode_condition.homopolymer_compress
34 --homopolymer-compress $mode_condition.homopolymer_compress 34 --homopolymer-compress $mode_condition.homopolymer_compress
35 #end if 35 #end if
36 $mode_condition.discover_paths 36 $mode_condition.discover_paths
37 $mode_condition.remove_terminal_gaps
37 -o dataset.$mode_condition.output_condition.out_format 38 -o dataset.$mode_condition.output_condition.out_format
38 #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz'] 39 #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz']
39 #if $mode_condition.output_condition.line_length 40 #if $mode_condition.output_condition.line_length
40 --line-length $mode_condition.output_condition.line_length 41 --line-length $mode_condition.output_condition.line_length
41 #end if 42 #end if
51 #else if $mode_condition.statistics_condition.selector == 'coordinates' 52 #else if $mode_condition.statistics_condition.selector == 'coordinates'
52 --out-coord $mode_condition.statistics_condition.out_coord 53 --out-coord $mode_condition.statistics_condition.out_coord
53 #else if $mode_condition.statistics_condition.selector == 'assembly' 54 #else if $mode_condition.statistics_condition.selector == 'assembly'
54 --nstar-report 55 --nstar-report
55 #else 56 #else
56 --seq-report 57 --segment-report
57 $mode_condition.statistics_condition.out_sequence 58 $mode_condition.statistics_condition.out_sequence
58 #end if 59 #end if
59 $mode_condition.locale 60 $mode_condition.locale
60 $mode_condition.discover_paths 61 $mode_condition.discover_paths
61 $mode_condition.tabular > '$stats' 62 $mode_condition.tabular > '$stats'
144 <option value="ascending">Ascending</option> 145 <option value="ascending">Ascending</option>
145 <option value="descending">Descending</option> 146 <option value="descending">Descending</option>
146 <option value="largest">Largest</option> 147 <option value="largest">Largest</option>
147 <option value="smallest">Smallest</option> 148 <option value="smallest">Smallest</option>
148 </param> 149 </param>
150 <param argument="--remove-terminal-gaps" type="boolean" truevalue="--remove-terminal-gaps" falsevalue="" checked="false" label="Remove gaps from the beginning and end of sequences"/>
149 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." /> 151 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." />
150 </when> 152 </when>
151 <when value="statistics"> 153 <when value="statistics">
152 <conditional name="statistics_condition"> 154 <conditional name="statistics_condition">
153 <param name="selector" type="select" label="Report mode"> 155 <param name="selector" type="select" label="Report mode">
154 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> 156 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option>
155 <option value="size">Scaffold, contig or gap sizes (--out-size)</option> 157 <option value="size">Scaffold, contig or gap sizes (--out-size)</option>
156 <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option> 158 <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option>
157 <option value="sequence">Sequence statistics (--seq-report)</option> 159 <option value="sequence">Sequence statistics (--segment-report)</option>
158 </param> 160 </param>
159 <when value="size"> 161 <when value="size">
160 <param argument="--out-size" type="select" label="Feature for reporting sizes" 162 <param argument="--out-size" type="select" label="Feature for reporting sizes"
161 help="Generate a tabular file with the sequence sizes"> 163 help="Generate a tabular file with the sequence sizes">
162 <option value="s">Scaffolds</option> 164 <option value="s">Scaffolds</option>
226 <param name="out_format" value="fasta.gz"/> 228 <param name="out_format" value="fasta.gz"/>
227 </conditional> 229 </conditional>
228 </conditional> 230 </conditional>
229 <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/> 231 <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/>
230 </test> 232 </test>
233 <!--Test 01 A) -->
234 <test expect_num_outputs="1">
235 <param name="input_file" value="dataset_01.fastq.gz"/>
236 <conditional name="mode_condition">
237 <param name="selector" value="manipulation"/>
238 <param name="swiss_army_knife" value="swiss_army.sak"/>
239 <param name="remove_terminal_gaps" value="true"/>
240 <conditional name="output_condition">
241 <param name="out_format" value="fasta.gz"/>
242 </conditional>
243 </conditional>
244 <output name="output" value="test_01_a.fasta.gz" ftype="fasta.gz"/>
245 </test>
231 <!--Test 02 --> 246 <!--Test 02 -->
232 <test expect_num_outputs="1"> 247 <test expect_num_outputs="1">
233 <param name="input_file" value="dataset_01.fastq.gz"/> 248 <param name="input_file" value="dataset_01.fastq.gz"/>
234 <conditional name="target_condition"> 249 <conditional name="target_condition">
235 <param name="target_condition" value="true"/> 250 <param name="target_condition" value="true"/>
416 **Assembly manipulation** 431 **Assembly manipulation**
417 432
418 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions. 433 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.
419 434
420 ]]></help> 435 ]]></help>
421 <expand macro="citations" /> 436 <expand macro="citations"/>
422 </tool> 437 </tool>