Mercurial > repos > bgruening > gfastats
comparison gfastats.xml @ 1:2b8b4cacb83d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
| author | bgruening |
|---|---|
| date | Mon, 25 Apr 2022 09:38:18 +0000 |
| parents | 5799092ffdff |
| children | ad1149b4f795 |
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| 0:5799092ffdff | 1:2b8b4cacb83d |
|---|---|
| 28 -k $mode_condition.swiss_army_knife | 28 -k $mode_condition.swiss_army_knife |
| 29 #end if | 29 #end if |
| 30 #if $mode_condition.sort | 30 #if $mode_condition.sort |
| 31 --sort $mode_condition.sort | 31 --sort $mode_condition.sort |
| 32 #end if | 32 #end if |
| 33 $mode_condition.homopolymer_compress | 33 #if $mode_condition.homopolymer_compress |
| 34 --homopolymer-compress $mode_condition.homopolymer_compress | |
| 35 #end if | |
| 34 -o dataset.$mode_condition.output_condition.out_format | 36 -o dataset.$mode_condition.output_condition.out_format |
| 35 #if $mode_condition.output_condition.out_format == 'fasta' | 37 #if $mode_condition.output_condition.out_format == 'fasta' |
| 36 #if $mode_condition.output_condition.line_length | 38 #if $mode_condition.output_condition.line_length |
| 37 --line-length $mode_condition.output_condition.line_length | 39 --line-length $mode_condition.output_condition.line_length |
| 38 #end if | 40 #end if |
| 39 #else if $mode_condition.output_condition.out_format == 'fasta.gz' | 41 #else if $mode_condition.output_condition.out_format == 'fasta.gz' |
| 40 #if $mode_condition.output_condition.line_length | 42 #if $mode_condition.output_condition.line_length |
| 41 --line-length $mode_condition.output_condition.line_length | 43 --line-length $mode_condition.output_condition.line_length |
| 42 #end if | 44 #end if |
| 43 #end if | 45 #end if |
| 44 #else | 46 #else if $mode_condition.selector == "statistics" |
| 45 #if $mode_condition.statistics_condition.selector == 'size' | 47 #if $mode_condition.statistics_condition.selector == 'size' |
| 46 --out-size $mode_condition.statistics_condition.out_size | 48 --out-size $mode_condition.statistics_condition.out_size |
| 47 #else if $mode_condition.statistics_condition.selector == 'coordinates' | 49 #else if $mode_condition.statistics_condition.selector == 'coordinates' |
| 48 --out-coord $mode_condition.statistics_condition.out_coord | 50 --out-coord $mode_condition.statistics_condition.out_coord |
| 49 #else if $mode_condition.statistics_condition.selector == 'assembly' | 51 #else if $mode_condition.statistics_condition.selector == 'assembly' |
| 50 --nstar-report | 52 --nstar-report |
| 51 #else | 53 #else |
| 52 --seq-report | 54 --seq-report |
| 53 $mode_condition.statistics_condition.out_sequence | 55 $mode_condition.statistics_condition.out_sequence |
| 54 #end if | 56 #end if |
| 55 $mode_condition.tabular > '$stats' | 57 $mode_condition.tabular > '$stats' |
| 58 #else | |
| 59 --agp-to-path $mode_condition.agp_to_path | |
| 60 $mode_condition.discover_paths | |
| 61 -o dataset.gfa | |
| 56 #end if | 62 #end if |
| 57 #if $mode_condition.selector == 'manipulation' | 63 #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding' |
| 58 && mv dataset* output_dataset | 64 && mv dataset* output_dataset |
| 59 #end if | 65 #end if |
| 60 ]]></command> | 66 ]]></command> |
| 61 <inputs> | 67 <inputs> |
| 62 <param name="input_file" argument="--fasta" type="data" | 68 <param name="input_file" argument="--fasta" type="data" |
| 93 </conditional> | 99 </conditional> |
| 94 <conditional name="mode_condition"> | 100 <conditional name="mode_condition"> |
| 95 <param name="selector" type="select" label="Tool mode"> | 101 <param name="selector" type="select" label="Tool mode"> |
| 96 <option value="statistics">Summary statistics generation</option> | 102 <option value="statistics">Summary statistics generation</option> |
| 97 <option value="manipulation">Genome assembly manipulation</option> | 103 <option value="manipulation">Genome assembly manipulation</option> |
| 104 <option value="scaffolding">Scaffolding</option> | |
| 98 </param> | 105 </param> |
| 99 <when value="manipulation"> | 106 <when value="manipulation"> |
| 100 <param argument="--swiss-army-knife" type="data" | 107 <param argument="--swiss-army-knife" type="data" |
| 101 format="text" label="SAK input file" optional="true" | 108 format="text" label="SAK input file" optional="true" |
| 102 help="Set of instructions provided as an ordered list"/> | 109 help="Set of instructions provided as an ordered list"/> |
| 126 <option value="ascending">Ascending</option> | 133 <option value="ascending">Ascending</option> |
| 127 <option value="descending">Descending</option> | 134 <option value="descending">Descending</option> |
| 128 <option value="largest">Largest</option> | 135 <option value="largest">Largest</option> |
| 129 <option value="smallest">Smallest</option> | 136 <option value="smallest">Smallest</option> |
| 130 </param> | 137 </param> |
| 131 <param argument="--homopolymer-compress" type="boolean" truevalue="--homopolymer-compress" falsevalue="" checked="false" | 138 <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 threshhold" /> |
| 132 label="Homopolymer compression" help="Compress all the homopolymers in the input"/> | |
| 133 </when> | 139 </when> |
| 134 <when value="statistics"> | 140 <when value="statistics"> |
| 135 <conditional name="statistics_condition"> | 141 <conditional name="statistics_condition"> |
| 136 <param name="selector" type="select" label="Report mode"> | 142 <param name="selector" type="select" label="Report mode"> |
| 137 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> | 143 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> |
| 165 </when> | 171 </when> |
| 166 </conditional> | 172 </conditional> |
| 167 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" | 173 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" |
| 168 label="Tabular-format output" help="Generate output in tabular format"/> | 174 label="Tabular-format output" help="Generate output in tabular format"/> |
| 169 </when> | 175 </when> |
| 176 <when value="scaffolding"> | |
| 177 <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" /> | |
| 178 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="generates the initial set of paths" help="In the graph space an assembly | |
| 179 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> | |
| 180 </when> | |
| 170 </conditional> | 181 </conditional> |
| 171 </inputs> | 182 </inputs> |
| 172 <outputs> | 183 <outputs> |
| 173 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats"> | 184 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats"> |
| 174 <filter>mode_condition['selector'] == 'statistics'</filter> | 185 <filter>mode_condition['selector'] == 'statistics'</filter> |
| 175 <change_format> | 186 <change_format> |
| 176 <when input="tabular" value="false" format="text"/> | 187 <when input="tabular" value="false" format="text"/> |
| 177 </change_format> | 188 </change_format> |
| 178 </data> | 189 </data> |
| 179 <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences"> | 190 <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences"> |
| 180 <filter>mode_condition['selector'] == 'manipulation'</filter> | 191 <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter> |
| 181 <change_format> | 192 <change_format> |
| 182 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/> | 193 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/> |
| 183 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/> | 194 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/> |
| 184 <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/> | 195 <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/> |
| 185 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/> | 196 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/> |
| 186 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/> | 197 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/> |
| 187 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/> | 198 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/> |
| 199 <when input="mode_condition.selector" value="scaffolding" format="gfa1"/> | |
| 188 </change_format> | 200 </change_format> |
| 189 </data> | 201 </data> |
| 190 </outputs> | 202 </outputs> |
| 191 <tests> | 203 <tests> |
| 192 <!--Test 01 --> | 204 <!--Test 01 --> |
| 286 <param name="selector" value="manipulation"/> | 298 <param name="selector" value="manipulation"/> |
| 287 <conditional name="output_condition"> | 299 <conditional name="output_condition"> |
| 288 <param name="out_format" value="fasta.gz"/> | 300 <param name="out_format" value="fasta.gz"/> |
| 289 </conditional> | 301 </conditional> |
| 290 <param name="sort" value="ascending"/> | 302 <param name="sort" value="ascending"/> |
| 291 <param name="homopolymer_compress" value="true"/> | |
| 292 </conditional> | 303 </conditional> |
| 293 <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/> | 304 <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/> |
| 305 </test> | |
| 306 <!--Test 09 --> | |
| 307 <test expect_num_outputs="1"> | |
| 308 <param name="input_file" value="dataset_03.fasta"/> | |
| 309 <conditional name="mode_condition"> | |
| 310 <param name="selector" value="manipulation"/> | |
| 311 <conditional name="output_condition"> | |
| 312 <param name="out_format" value="fasta.gz"/> | |
| 313 </conditional> | |
| 314 <param name="homopolymer_compress" value="10"/> | |
| 315 </conditional> | |
| 316 <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/> | |
| 317 </test> | |
| 318 <!--Test 10 --> | |
| 319 <test expect_num_outputs="1"> | |
| 320 <param name="input_file" value="dataset_04.gfa"/> | |
| 321 <conditional name="mode_condition"> | |
| 322 <param name="selector" value="scaffolding"/> | |
| 323 <param name="agp_to_path" value="dataset_05.agp"/> | |
| 324 <param name="discover_paths" value="true"/> | |
| 325 </conditional> | |
| 326 <output name="output" value="test_10.gfa" ftype="gfa1"/> | |
| 294 </test> | 327 </test> |
| 295 </tests> | 328 </tests> |
| 296 <help><![CDATA[ | 329 <help><![CDATA[ |
| 297 | 330 |
| 298 .. class:: infomark | 331 .. class:: infomark |