Mercurial > repos > iuc > mothur_remove_lineage
comparison remove.lineage.xml @ 2:d46157fb52cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:06:50 -0400 |
| parents | 5a18d3d09b80 |
| children |
comparison
equal
deleted
inserted
replaced
| 1:35665dcf7f18 | 2:d46157fb52cd |
|---|---|
| 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 #import re | 12 #import re |
| 13 ## create symlinks to input datasets | 13 ## create symlinks to input datasets |
| 14 ln -s "$file.taxonomy" file.taxonomy.dat && | 14 ln -s '$file.taxonomy' file.taxonomy.dat && |
| 15 #if $file.filetype == "useconstaxonomy": | 15 #if $file.filetype == "useconstaxonomy": |
| 16 ln -s "$file.shared" file.shared.dat && | 16 ln -s '$file.shared' file.shared.dat && |
| 17 ln -s "$file.list" file.list.dat && | 17 ln -s '$file.list' file.list.dat && |
| 18 #end if | |
| 19 ln -s '$fasta_in' fasta_in.dat && | |
| 20 ln -s '$group_in' group_in.dat && | |
| 21 ln -s '$alignreport_in' alignreport_in.dat && | |
| 22 ln -s '$list_in' list_in.dat && | |
| 23 ln -s '$name_in' name_in.dat && | |
| 24 ln -s '$count' count.dat && | |
| 25 | |
| 26 echo 'remove.lineage( | |
| 27 #if $file.filetype == "usetaxonomy": | |
| 28 taxonomy=file.taxonomy.dat | |
| 29 #else | |
| 30 constaxonomy=file.taxonomy.dat | |
| 31 #if $file.shared: | |
| 32 ,shared=file.shared.dat | |
| 18 #end if | 33 #end if |
| 19 ln -s "$fasta_in" fasta_in.dat && | 34 #if $file.list: |
| 20 ln -s "$group_in" group_in.dat && | 35 ,list=file.list.dat |
| 21 ln -s "$alignreport_in" alignreport_in.dat && | 36 #end if |
| 22 ln -s "$list_in" list_in.dat && | 37 #end if |
| 23 ln -s "$name_in" name_in.dat && | 38 #if $file.taxons: |
| 24 ln -s "$count" count.dat && | 39 #set taxonstring=str($file.taxons).replace(",","-") |
| 25 | 40 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' |
| 26 echo 'remove.lineage( | 41 #elif $taxon: |
| 27 #if $file.filetype == "usetaxonomy": | 42 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' |
| 28 taxonomy=file.taxonomy.dat | 43 #end if |
| 29 #else | 44 #if $fasta_in: |
| 30 constaxonomy=file.taxonomy.dat | 45 ,fasta=fasta_in.dat |
| 31 #if $file.shared: | 46 #end if |
| 32 ,shared=file.shared.dat | 47 #if $group_in: |
| 33 #end if | 48 ,group=group_in.dat |
| 34 #if $file.list: | 49 #end if |
| 35 ,list=file.list.dat | 50 #if $alignreport_in: |
| 36 #end if | 51 ,alignreport=alignreport_in.dat |
| 37 #end if | 52 #end if |
| 38 #if $file.taxons: | 53 #if $list_in: |
| 39 #set taxonstring=str($file.taxons).replace(",","-") | 54 ,list=list_in.dat |
| 40 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' | 55 #end if |
| 41 #elif $taxon: | 56 #if $name_in: |
| 42 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' | 57 ,name=name_in.dat |
| 43 #end if | 58 ,dups=$dups |
| 44 #if $fasta_in: | 59 #end if |
| 45 ,fasta=fasta_in.dat | 60 #if $count: |
| 46 #end if | 61 ,count=count.dat |
| 47 #if $group_in: | 62 #end if |
| 48 ,group=group_in.dat | 63 )' |
| 49 #end if | 64 | sed 's/ //g' ## mothur trips over whitespace |
| 50 #if $alignreport_in: | 65 | mothur |
| 51 ,alignreport=alignreport_in.dat | 66 | tee mothur.out.log |
| 52 #end if | |
| 53 #if $list_in: | |
| 54 ,list=list_in.dat | |
| 55 #end if | |
| 56 #if $name_in: | |
| 57 ,name=name_in.dat | |
| 58 ,dups=$dups | |
| 59 #end if | |
| 60 #if $count: | |
| 61 ,count=count.dat | |
| 62 #end if | |
| 63 )' | |
| 64 | sed 's/ //g' ## mothur trips over whitespace | |
| 65 | mothur | |
| 66 | tee mothur.out.log | |
| 67 ]]></command> | 67 ]]></command> |
| 68 <inputs> | 68 <inputs> |
| 69 <conditional name="file"> | 69 <conditional name="file"> |
| 70 <param name="filetype" type="select" label="choose which file is used"> | 70 <param name="filetype" type="select" label="choose which file is used"> |
| 71 <option value="usetaxonomy" selected="true">taxonomy</option> | 71 <option value="usetaxonomy" selected="true">taxonomy</option> |
| 118 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> | 118 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> |
| 119 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> | 119 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> |
| 120 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> | 120 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> |
| 121 <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/> | 121 <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/> |
| 122 <param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/> | 122 <param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/> |
| 123 <expand macro="param-savelog"/> | |
| 123 </inputs> | 124 </inputs> |
| 124 <outputs> | 125 <outputs> |
| 125 <expand macro="logfile-output"/> | 126 <expand macro="logfile-output"/> |
| 126 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/> | 127 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/> |
| 127 <data format_source="fasta_in" name="fasta_out" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> | 128 <data format_source="fasta_in" name="fasta_out" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> |
| 188 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/> | 189 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/> |
| 189 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/> | 190 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/> |
| 190 <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/> | 191 <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/> |
| 191 </test> | 192 </test> |
| 192 </tests> | 193 </tests> |
| 193 <help> | 194 <help><![CDATA[ |
| 194 <![CDATA[ | |
| 195 | 195 |
| 196 @MOTHUR_OVERVIEW@ | 196 @MOTHUR_OVERVIEW@ |
| 197 | 197 |
| 198 **Command Documentation** | 198 **Command Documentation** |
| 199 | 199 |
| 204 .. _group: https://www.mothur.org/wiki/Group_file | 204 .. _group: https://www.mothur.org/wiki/Group_file |
| 205 .. _list: https://www.mothur.org/wiki/List_file | 205 .. _list: https://www.mothur.org/wiki/List_file |
| 206 .. _align.report: https://www.mothur.org/wiki/Align.seqs | 206 .. _align.report: https://www.mothur.org/wiki/Align.seqs |
| 207 .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage | 207 .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage |
| 208 | 208 |
| 209 ]]> | 209 ]]></help> |
| 210 </help> | |
| 211 <expand macro="citations"/> | 210 <expand macro="citations"/> |
| 212 </tool> | 211 </tool> |