Mercurial > repos > iuc > mothur_bin_seqs
comparison bin.seqs.xml @ 3:82c917a4ed55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:07:19 -0400 |
| parents | 905ff5f3e91d |
| children |
comparison
equal
deleted
inserted
replaced
| 2:905ff5f3e91d | 3:82c917a4ed55 |
|---|---|
| 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 "$name" name.dat && | 13 ln -s '$name' name.dat && |
| 14 ln -s "$group" group.dat && | 14 ln -s '$group' group.dat && |
| 15 ln -s "$fasta" fasta.dat && | 15 ln -s '$fasta' fasta.dat && |
| 16 ln -s "$otu" otu.dat && | 16 ln -s '$otu' otu.dat && |
| 17 ln -s "$count" count.dat && | 17 ln -s '$count' count.dat && |
| 18 | 18 |
| 19 echo 'bin.seqs( | 19 echo 'bin.seqs( |
| 20 #if $name: | 20 #if $name: |
| 21 name=name.dat, | 21 name=name.dat, |
| 22 #end if | 22 #end if |
| 23 #if $group: | 23 #if $group: |
| 24 group=group.dat, | 24 group=group.dat, |
| 25 #end if | 25 #end if |
| 26 #if $label: | 26 #if $label: |
| 27 label=${ str($label).replace(",","-") }, | 27 label=${ str($label).replace(",","-") }, |
| 28 #end if | 28 #end if |
| 29 #if $count: | 29 #if $count: |
| 30 count=count.dat, | 30 count=count.dat, |
| 31 #end if | 31 #end if |
| 32 fasta=fasta.dat, | 32 fasta=fasta.dat, |
| 33 list=otu.dat | 33 list=otu.dat |
| 34 )' | 34 )' |
| 35 | sed 's/ //g' ## mothur trips over whitespace | 35 | sed 's/ //g' ## mothur trips over whitespace |
| 36 | mothur | 36 | mothur |
| 37 | tee mothur.out.log | 37 | tee mothur.out.log |
| 38 ]]></command> | 38 ]]></command> |
| 39 <inputs> | 39 <inputs> |
| 40 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> | 40 <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> |
| 41 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> | 41 <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List"/> |
| 42 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> | 42 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> |
| 43 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 43 <param argument="label" type="select" multiple="true" label="label - OTU Labels"> |
| 44 <expand macro="labeloptions"/> | 44 <expand macro="labeloptions"/> |
| 45 </param> | 45 </param> |
| 46 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> | 46 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> |
| 47 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/> | 47 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table" |
| 48 help="Represents the number of duplicate sequences for a given representitive sequence"/> | |
| 49 <expand macro="param-savelog"/> | |
| 48 </inputs> | 50 </inputs> |
| 49 <outputs> | 51 <outputs> |
| 50 <expand macro="logfile-output"/> | 52 <expand macro="logfile-output"/> |
| 51 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label"> | 53 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label"> |
| 52 <discover_datasets pattern=".*?\.(?P<designation>.*)\.fasta" format="fasta"/> | 54 <discover_datasets pattern=".*?\.(?P<designation>.*)\.fasta" format="fasta"/> |
| 55 <tests> | 57 <tests> |
| 56 <test><!-- test with defaults --> | 58 <test><!-- test with defaults --> |
| 57 <param name="otu" value="amazon.an.list"/> | 59 <param name="otu" value="amazon.an.list"/> |
| 58 <param name="fasta" value="amazon.fasta"/> | 60 <param name="fasta" value="amazon.fasta"/> |
| 59 <output_collection name="fastafiles" count="36"> | 61 <output_collection name="fastafiles" count="36"> |
| 60 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/> | 62 <element name="0.22" ftype="fasta"> |
| 63 <assert_contents> | |
| 64 <expand macro="test-fasta-format"/> | |
| 65 <has_text text="U68589"/> | |
| 66 </assert_contents> | |
| 67 </element> | |
| 61 </output_collection> | 68 </output_collection> |
| 69 <param name="savelog" value="true"/> | |
| 62 <expand macro="logfile-test"/> | 70 <expand macro="logfile-test"/> |
| 63 </test> | 71 </test> |
| 64 <test><!-- test with group and name file and label select --> | 72 <test><!-- test with group and name file and label select --> |
| 65 <param name="otu" value="amazon.an.list"/> | 73 <param name="otu" value="amazon.an.list"/> |
| 66 <param name="fasta" value="amazon.fasta"/> | 74 <param name="fasta" value="amazon.fasta"/> |
| 67 <param name="name" value="amazon.names"/> | 75 <param name="name" value="amazon.names"/> |
| 68 <param name="group" value="amazon.groups" ftype="mothur.groups"/> | 76 <param name="group" value="amazon.groups" ftype="mothur.groups"/> |
| 69 <param name="label" value="0.03,0.05,0.22"/> | 77 <param name="label" value="0.03,0.05,0.22"/> |
| 70 <output_collection name="fastafiles" count="3"> | 78 <output_collection name="fastafiles" count="3"> |
| 71 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/> | 79 <element name="0.22" ftype="fasta"> |
| 80 <assert_contents> | |
| 81 <expand macro="test-fasta-format"/> | |
| 82 <has_text text="U68589"/> | |
| 83 </assert_contents> | |
| 84 </element> | |
| 72 </output_collection> | 85 </output_collection> |
| 86 <param name="savelog" value="true"/> | |
| 73 <expand macro="logfile-test"/> | 87 <expand macro="logfile-test"/> |
| 74 </test> | 88 </test> |
| 75 </tests> | 89 </tests> |
| 76 <help> | 90 <help><![CDATA[ |
| 77 <![CDATA[ | |
| 78 | 91 |
| 79 @MOTHUR_OVERVIEW@ | 92 @MOTHUR_OVERVIEW@ |
| 80 | 93 |
| 81 **Command Documentation** | 94 **Command Documentation** |
| 82 | 95 |
| 83 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. | 96 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU |
| 97 from the list_file_ that they belong to. Such an output may be helpful for generating primers specific | |
| 98 to an OTU or for classification of sequences. | |
| 84 | 99 |
| 85 .. _list_file: https://www.mothur.org/wiki/List_file | 100 .. _list_file: https://www.mothur.org/wiki/List_file |
| 86 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs | 101 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs |
| 87 ]]> | 102 |
| 88 </help> | 103 ]]></help> |
| 89 <expand macro="citations"/> | 104 <expand macro="citations"/> |
| 90 </tool> | 105 </tool> |