Mercurial > repos > iuc > mothur_sffinfo
comparison sffinfo.xml @ 2:13d1e5e44a91 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:19:08 -0400 |
| parents | 5ada2d00e874 |
| children | 51d7c2486a68 |
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| 1:5d52096c0a9c | 2:13d1e5e44a91 |
|---|---|
| 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 "$sff" sff.dat && | 13 ln -s '$sff' sff.dat && |
| 14 ln -s "$accnos" accnos.dat && | 14 ln -s '$accnos' accnos.dat && |
| 15 #if $oligo.add == "yes": | 15 #if $oligo.add == "yes": |
| 16 ln -s "$oligo.oligos" oligo.oligos.dat && | 16 ln -s '$oligo.oligos' oligo.oligos.dat && |
| 17 #end if | 17 #end if |
| 18 | 18 |
| 19 echo 'sffinfo( | 19 echo 'sffinfo( |
| 20 sff=sff.dat, | 20 sff=sff.dat, |
| 21 fasta=$fasta, | 21 fasta=$fasta, |
| 22 qfile=$qfile, | 22 qfile=$qfile, |
| 23 $sfftxt | 23 $sfftxt |
| 24 flow=$flow, | 24 flow=$flow, |
| 25 trim=$trim | 25 trim=$trim |
| 26 #if $accnos: | 26 #if $accnos: |
| 27 ,accnos=accnos.dat | 27 ,accnos=accnos.dat |
| 28 #end if | 28 #end if |
| 29 #if $oligo.add == "yes": | 29 #if $oligo.add == "yes": |
| 30 ,oligos=oligo.oligos.dat | 30 ,oligos=oligo.oligos.dat |
| 31 ,bdiffs=$oligo.bdiffs | 31 ,bdiffs=$oligo.bdiffs |
| 32 ,pdiffs=$oligo.pdiffs | 32 ,pdiffs=$oligo.pdiffs |
| 33 ,tdiffs=$oligo.tdiffs | 33 ,tdiffs=$oligo.tdiffs |
| 34 ,ldiffs=$oligo.ldiffs | 34 ,ldiffs=$oligo.ldiffs |
| 35 ,sdiffs=$oligo.sdiffs | 35 ,sdiffs=$oligo.sdiffs |
| 36 #end if | 36 #end if |
| 37 )' | 37 )' |
| 38 | sed 's/ //g' ## mothur trips over whitespace | 38 | sed 's/ //g' ## mothur trips over whitespace |
| 39 | mothur | 39 | mothur |
| 40 | tee mothur.out.log | 40 | tee mothur.out.log |
| 41 ]]></command> | 41 ]]></command> |
| 42 <inputs> | 42 <inputs> |
| 43 <param name="sff" type="data" format="sff" label="sff - Sff data"/> | 43 <param name="sff" type="data" format="sff" label="sff - Sff data"/> |
| 44 <conditional name="oligo"> | 44 <conditional name="oligo"> |
| 45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file."> | 45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file."> |
| 60 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/> | 60 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/> |
| 61 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/> | 61 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/> |
| 62 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/> | 62 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/> |
| 63 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/> | 63 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/> |
| 64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/> | 64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/> |
| 65 <expand macro="param-savelog"/> | |
| 65 </inputs> | 66 </inputs> |
| 66 <outputs> | 67 <outputs> |
| 67 <expand macro="logfile-output"/> | 68 <expand macro="logfile-output"/> |
| 68 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"> | 69 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"> |
| 69 <filter>fasta</filter> | 70 <filter>fasta</filter> |
| 87 <param name="sfftxt" value="true"/> | 88 <param name="sfftxt" value="true"/> |
| 88 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/> | 89 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/> |
| 89 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> | 90 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> |
| 90 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/> | 91 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/> |
| 91 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> | 92 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> |
| 93 <param name="savelog" value="true"/> | |
| 92 <expand macro="logfile-test"/> | 94 <expand macro="logfile-test"/> |
| 93 </test> | 95 </test> |
| 94 <test><!-- test with oligos file --> | 96 <test><!-- test with oligos file --> |
| 95 <param name="sff" value="Fasting_Example1.sff"/> | 97 <param name="sff" value="Fasting_Example1.sff"/> |
| 96 <param name="add" value="yes"/> | 98 <param name="add" value="yes"/> |
| 97 <param name="oligos" value="GQY1XT001.oligos"/> | 99 <param name="oligos" value="GQY1XT001.oligos"/> |
| 98 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/> | 100 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/> |
| 99 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> | 101 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> |
| 100 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> | 102 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> |
| 101 <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/> | 103 <output name="out_scrap" file="Fasting_Example1.scrap.sff" ftype="sff" compare="sim_size"/> |
| 104 <param name="savelog" value="true"/> | |
| 102 <expand macro="logfile-test"/> | 105 <expand macro="logfile-test"/> |
| 103 </test> | 106 </test> |
| 104 </tests> | 107 </tests> |
| 105 <help> | 108 <help><![CDATA[ |
| 106 <![CDATA[ | |
| 107 | 109 |
| 108 @MOTHUR_OVERVIEW@ | 110 @MOTHUR_OVERVIEW@ |
| 109 | 111 |
| 110 **Command Documentation** | 112 **Command Documentation** |
| 111 | 113 |
| 112 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. | 114 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. |
| 113 | 115 |
| 114 | 116 |
| 115 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo | 117 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo |
| 116 ]]> | 118 |
| 117 </help> | 119 ]]></help> |
| 118 <expand macro="citations"/> | 120 <expand macro="citations"/> |
| 119 </tool> | 121 </tool> |