Mercurial > repos > iuc > mothur_split_abund
comparison split.abund.xml @ 2:407a5352f0ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:01:54 -0400 |
| parents | b15d9a2d2311 |
| children | ff3e693f8d4d |
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| 1:ede016062913 | 2:407a5352f0ec |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
| 11 | 11 |
| 12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
| 13 ln -s "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
| 14 ln -s "$search.input" search_input.dat && | 14 ln -s '$search.input' search_input.dat && |
| 15 #if $split.dosplit == "yes": | 15 #if $split.dosplit == "yes": |
| 16 ln -s "$split.group" split_group.dat && | 16 ln -s '$split.group' split_group.dat && |
| 17 #end if | |
| 18 | |
| 19 echo 'split.abund( | |
| 20 fasta=fasta.dat, | |
| 21 #if $search.type == "list": | |
| 22 list=search_input.dat, | |
| 23 #if $search.label: | |
| 24 label=${ str($search.label).replace(",","-") }, | |
| 17 #end if | 25 #end if |
| 18 | 26 #elif $search.type == "name": |
| 19 echo 'split.abund( | 27 name=search_input.dat, |
| 20 fasta=fasta.dat, | 28 #else |
| 21 #if $search.type == "list": | 29 count=search_input.dat, |
| 22 list=search_input.dat, | 30 #end if |
| 23 #if $search.label: | 31 #if $split.dosplit == "yes": |
| 24 label=${ str($search.label).replace(",","-") }, | 32 #if $split.group: |
| 25 #end if | 33 group=split_group.dat, |
| 26 #elif $search.type == "name": | 34 #end if |
| 27 name=search_input.dat, | 35 #if $split.groups: |
| 28 #else | 36 groups=${ str($split.groups).replace(",","-") }, |
| 29 count=search_input.dat, | 37 #end if |
| 30 #end if | 38 #end if |
| 31 #if $split.dosplit == "yes": | 39 accnos=$accnos, |
| 32 #if $split.group: | 40 cutoff=$cutoff |
| 33 group=split_group.dat, | 41 )' |
| 34 #end if | 42 | sed 's/ //g' ## mothur trips over whitespace |
| 35 #if $split.groups: | 43 | mothur |
| 36 groups=${ str($split.groups).replace(",","-") }, | 44 | tee mothur.out.log |
| 37 #end if | |
| 38 #end if | |
| 39 accnos=$accnos, | |
| 40 cutoff=$cutoff | |
| 41 )' | |
| 42 | sed 's/ //g' ## mothur trips over whitespace | |
| 43 | mothur | |
| 44 | tee mothur.out.log | |
| 45 ]]></command> | 45 ]]></command> |
| 46 <inputs> | 46 <inputs> |
| 47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> | 47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> |
| 48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> | 48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> |
| 49 <conditional name="search"> | 49 <conditional name="search"> |
| 81 </param> | 81 </param> |
| 82 </when> | 82 </when> |
| 83 <when value="no"/> | 83 <when value="no"/> |
| 84 </conditional> | 84 </conditional> |
| 85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/> | 85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/> |
| 86 <expand macro="param-savelog"/> | |
| 86 </inputs> | 87 </inputs> |
| 87 <outputs> | 88 <outputs> |
| 88 <expand macro="logfile-output"/> | 89 <expand macro="logfile-output"/> |
| 89 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta"> | 90 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta"> |
| 90 <filter>search['type'] != 'list'</filter> | 91 <filter>search['type'] != 'list'</filter> |
| 168 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> | 169 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> |
| 169 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/> | 170 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/> |
| 170 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/> | 171 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/> |
| 171 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> | 172 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> |
| 172 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> | 173 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> |
| 174 <param name="savelog" value="true"/> | |
| 173 <expand macro="logfile-test"/> | 175 <expand macro="logfile-test"/> |
| 174 </test> | 176 </test> |
| 175 <test><!-- test with name file and accnos output --> | 177 <test><!-- test with name file and accnos output --> |
| 176 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | 178 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
| 177 <param name="type" value="name"/> | 179 <param name="type" value="name"/> |
| 182 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> | 184 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> |
| 183 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/> | 185 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/> |
| 184 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/> | 186 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/> |
| 185 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> | 187 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> |
| 186 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> | 188 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> |
| 189 <param name="savelog" value="true"/> | |
| 187 <expand macro="logfile-test"/> | 190 <expand macro="logfile-test"/> |
| 188 </test> | 191 </test> |
| 189 <test><!-- test with name file and accnos output with groups--> | 192 <test><!-- test with name file and accnos output with groups--> |
| 190 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | 193 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
| 191 <param name="type" value="name"/> | 194 <param name="type" value="name"/> |
| 217 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/> | 220 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/> |
| 218 </output_collection> | 221 </output_collection> |
| 219 <output_collection name="rare_groups_coll" count="2"> | 222 <output_collection name="rare_groups_coll" count="2"> |
| 220 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/> | 223 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/> |
| 221 </output_collection> | 224 </output_collection> |
| 225 <param name="savelog" value="true"/> | |
| 222 <expand macro="logfile-test"/> | 226 <expand macro="logfile-test"/> |
| 223 </test> | 227 </test> |
| 224 <test><!-- test with list --> | 228 <test><!-- test with list --> |
| 225 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | 229 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
| 226 <param name="type" value="list"/> | 230 <param name="type" value="list"/> |
| 252 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> | 256 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> |
| 253 </output_collection> | 257 </output_collection> |
| 254 <output_collection name="rare_groups_coll" count="72"> | 258 <output_collection name="rare_groups_coll" count="72"> |
| 255 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/> | 259 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/> |
| 256 </output_collection> | 260 </output_collection> |
| 261 <param name="savelog" value="true"/> | |
| 257 <expand macro="logfile-test"/> | 262 <expand macro="logfile-test"/> |
| 258 </test> | 263 </test> |
| 259 <test><!-- test with list and label and group select--> | 264 <test><!-- test with list and label and group select--> |
| 260 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | 265 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
| 261 <param name="type" value="list"/> | 266 <param name="type" value="list"/> |
| 288 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> | 293 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> |
| 289 </output_collection> | 294 </output_collection> |
| 290 <output_collection name="rare_groups_coll" count="4"> | 295 <output_collection name="rare_groups_coll" count="4"> |
| 291 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/> | 296 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/> |
| 292 </output_collection> | 297 </output_collection> |
| 298 <param name="savelog" value="true"/> | |
| 293 <expand macro="logfile-test"/> | 299 <expand macro="logfile-test"/> |
| 294 </test> | 300 </test> |
| 295 </tests> | 301 </tests> |
| 296 <help> | 302 <help><![CDATA[ |
| 297 <![CDATA[ | |
| 298 | 303 |
| 299 @MOTHUR_OVERVIEW@ | 304 @MOTHUR_OVERVIEW@ |
| 300 | 305 |
| 301 **Command Documentation** | 306 **Command Documentation** |
| 302 | 307 |
| 303 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups. | 308 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups. |
| 304 | 309 |
| 305 .. _list: https://www.mothur.org/wiki/List_file | 310 .. _list: https://www.mothur.org/wiki/List_file |
| 306 .. _name: https://www.mothur.org/wiki/Name_file | 311 .. _name: https://www.mothur.org/wiki/Name_file |
| 307 .. _split.abund: https://www.mothur.org/wiki/Split.abund | 312 .. _split.abund: https://www.mothur.org/wiki/Split.abund |
| 308 ]]> | 313 |
| 309 </help> | 314 ]]></help> |
| 310 <expand macro="citations"/> | 315 <expand macro="citations"/> |
| 311 </tool> | 316 </tool> |